From 561537c4dea080409bf0c0dd8a2b7b57c327a0fe Mon Sep 17 00:00:00 2001
From: jeanrjc <jean.cury@normalesup.org>
Date: Wed, 10 Jan 2024 11:59:04 +0100
Subject: [PATCH] replace .pdb with .cif
---
content/3.defense-systems/abia.md | 6 +-
content/3.defense-systems/abib.md | 2 +-
content/3.defense-systems/abic.md | 2 +-
content/3.defense-systems/abid.md | 2 +-
content/3.defense-systems/abie.md | 4 +-
content/3.defense-systems/abig.md | 4 +-
content/3.defense-systems/abih.md | 2 +-
content/3.defense-systems/abii.md | 2 +-
content/3.defense-systems/abij.md | 2 +-
content/3.defense-systems/abik.md | 2 +-
content/3.defense-systems/abil.md | 4 +-
content/3.defense-systems/abin.md | 2 +-
content/3.defense-systems/abio.md | 2 +-
content/3.defense-systems/abip2.md | 2 +-
content/3.defense-systems/abiq.md | 2 +-
content/3.defense-systems/abir.md | 6 +-
content/3.defense-systems/abit.md | 4 +-
content/3.defense-systems/abiu.md | 2 +-
content/3.defense-systems/abiv.md | 2 +-
content/3.defense-systems/abiz.md | 2 +-
content/3.defense-systems/aditi.md | 4 +-
content/3.defense-systems/avs.md | 16 +--
content/3.defense-systems/azaca.md | 6 +-
content/3.defense-systems/borvo.md | 2 +-
content/3.defense-systems/brex.md | 38 +++---
content/3.defense-systems/bsta.md | 6 +-
content/3.defense-systems/bunzi.md | 4 +-
.../3.defense-systems/butters_gp30_gp31.md | 4 +-
content/3.defense-systems/butters_gp57r.md | 2 +-
content/3.defense-systems/caprel.md | 2 +-
content/3.defense-systems/cas.md | 110 +++++++++---------
content/3.defense-systems/cbass.md | 32 ++---
content/3.defense-systems/charlie_gp32.md | 2 +-
content/3.defense-systems/dartg.md | 4 +-
content/3.defense-systems/dazbog.md | 8 +-
content/3.defense-systems/dctpdeaminase.md | 2 +-
content/3.defense-systems/ddmde.md | 4 +-
content/3.defense-systems/detocs.md | 12 +-
content/3.defense-systems/dgtpase.md | 2 +-
content/3.defense-systems/disarm.md | 20 ++--
content/3.defense-systems/dnd.md | 28 ++---
content/3.defense-systems/dodola.md | 4 +-
content/3.defense-systems/dpd.md | 24 ++--
content/3.defense-systems/drt.md | 22 ++--
content/3.defense-systems/druantia.md | 22 ++--
content/3.defense-systems/dsr.md | 4 +-
content/3.defense-systems/eleos.md | 4 +-
content/3.defense-systems/fs_giy_yig.md | 2 +-
content/3.defense-systems/fs_hepn_tm.md | 4 +-
content/3.defense-systems/fs_hp.md | 2 +-
content/3.defense-systems/fs_hp_sdh_sah.md | 4 +-
content/3.defense-systems/fs_hsdr_like.md | 4 +-
content/3.defense-systems/fs_sma.md | 2 +-
content/3.defense-systems/gabija.md | 4 +-
content/3.defense-systems/gao_ape.md | 2 +-
content/3.defense-systems/gao_her.md | 8 +-
content/3.defense-systems/gao_hhe.md | 2 +-
content/3.defense-systems/gao_iet.md | 4 +-
content/3.defense-systems/gao_mza.md | 10 +-
content/3.defense-systems/gao_ppl.md | 2 +-
content/3.defense-systems/gao_qat.md | 8 +-
content/3.defense-systems/gao_rl.md | 8 +-
content/3.defense-systems/gao_tery.md | 6 +-
content/3.defense-systems/gao_tmn.md | 2 +-
content/3.defense-systems/gao_upx.md | 2 +-
content/3.defense-systems/gaps1.md | 2 +-
content/3.defense-systems/gaps2.md | 2 +-
content/3.defense-systems/gaps4.md | 4 +-
content/3.defense-systems/gaps6.md | 4 +-
content/3.defense-systems/gasdermin.md | 12 +-
content/3.defense-systems/hachiman.md | 4 +-
content/3.defense-systems/hna.md | 2 +-
content/3.defense-systems/isg15-like.md | 40 +++----
content/3.defense-systems/jukab.md | 4 +-
content/3.defense-systems/kiwa.md | 4 +-
content/3.defense-systems/lamassu-fam.md | 66 +++++------
content/3.defense-systems/lit.md | 2 +-
content/3.defense-systems/mads.md | 14 +--
content/3.defense-systems/menshen.md | 6 +-
content/3.defense-systems/mmb_gp29_gp30.md | 4 +-
content/3.defense-systems/mok_hok_sok.md | 2 +-
content/3.defense-systems/mokosh.md | 6 +-
content/3.defense-systems/nhi.md | 2 +-
content/3.defense-systems/nixi.md | 2 +-
content/3.defense-systems/nlr.md | 4 +-
content/3.defense-systems/old_exonuclease.md | 2 +-
content/3.defense-systems/olokun.md | 4 +-
content/3.defense-systems/pago.md | 18 +--
content/3.defense-systems/panchino_gp28.md | 2 +-
content/3.defense-systems/paris.md | 12 +-
content/3.defense-systems/pd-lambda-1.md | 2 +-
content/3.defense-systems/pd-lambda-2.md | 6 +-
content/3.defense-systems/pd-lambda-3.md | 6 +-
content/3.defense-systems/pd-lambda-4.md | 4 +-
content/3.defense-systems/pd-lambda-5.md | 4 +-
content/3.defense-systems/pd-lambda-6.md | 2 +-
content/3.defense-systems/pd-t4-1.md | 2 +-
content/3.defense-systems/pd-t4-10.md | 4 +-
content/3.defense-systems/pd-t4-2.md | 4 +-
content/3.defense-systems/pd-t4-3.md | 2 +-
content/3.defense-systems/pd-t4-4.md | 4 +-
content/3.defense-systems/pd-t4-5.md | 2 +-
content/3.defense-systems/pd-t4-6.md | 2 +-
content/3.defense-systems/pd-t4-7.md | 2 +-
content/3.defense-systems/pd-t4-8.md | 2 +-
content/3.defense-systems/pd-t4-9.md | 6 +-
content/3.defense-systems/pd-t7-1.md | 2 +-
content/3.defense-systems/pd-t7-2.md | 4 +-
content/3.defense-systems/pd-t7-3.md | 2 +-
content/3.defense-systems/pd-t7-4.md | 2 +-
content/3.defense-systems/pd-t7-5.md | 2 +-
content/3.defense-systems/pfiat.md | 4 +-
content/3.defense-systems/pif.md | 4 +-
content/3.defense-systems/prrc.md | 8 +-
content/3.defense-systems/psyrta.md | 4 +-
content/3.defense-systems/pycsar.md | 8 +-
content/3.defense-systems/radar.md | 10 +-
content/3.defense-systems/retron.md | 32 ++---
content/3.defense-systems/rexab.md | 4 +-
content/3.defense-systems/rloc.md | 2 +-
content/3.defense-systems/rnlab.md | 4 +-
content/3.defense-systems/rosmerta.md | 4 +-
content/3.defense-systems/rst_2tm_1tm_tir.md | 6 +-
content/3.defense-systems/rst_3hp.md | 6 +-
content/3.defense-systems/rst_duf4238.md | 2 +-
content/3.defense-systems/rst_gop_beta_cll.md | 6 +-
.../3.defense-systems/rst_helicaseduf2290.md | 4 +-
.../3.defense-systems/rst_hydrolase-3tm.md | 4 +-
.../3.defense-systems/rst_rt-nitrilase-tm.md | 4 +-
content/3.defense-systems/rst_tir-nlr.md | 2 +-
content/3.defense-systems/sanata.md | 4 +-
content/3.defense-systems/sefir.md | 2 +-
content/3.defense-systems/septu.md | 8 +-
content/3.defense-systems/shango.md | 6 +-
content/3.defense-systems/shedu.md | 2 +-
content/3.defense-systems/shosta.md | 4 +-
content/3.defense-systems/sofic.md | 2 +-
content/3.defense-systems/spbk.md | 2 +-
content/3.defense-systems/sspbcde.md | 20 ++--
content/3.defense-systems/stk2.md | 2 +-
content/3.defense-systems/thoeris.md | 8 +-
content/3.defense-systems/tiamat.md | 2 +-
content/3.defense-systems/uzume.md | 2 +-
content/3.defense-systems/viperin.md | 2 +-
content/3.defense-systems/wadjet.md | 24 ++--
content/3.defense-systems/zorya.md | 14 +--
146 files changed, 516 insertions(+), 516 deletions(-)
diff --git a/content/3.defense-systems/abia.md b/content/3.defense-systems/abia.md
index e0fba523..7159f29a 100644
--- a/content/3.defense-systems/abia.md
+++ b/content/3.defense-systems/abia.md
@@ -53,7 +53,7 @@ Proportion of genome encoding the AbiA system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abia/AbiA_large__AbiA_large.pdb
+ - /abia/AbiA_large__AbiA_large.cif
---
::
@@ -64,8 +64,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /abia/AbiA_small.AbiA_small__AbiA_small.0.DF.pdb
- - /abia/AbiA_small.AbiA_small__AbiA_SLATT.0.DF.pdb
+ - /abia/AbiA_small.AbiA_small__AbiA_small.0.DF.cif
+ - /abia/AbiA_small.AbiA_small__AbiA_SLATT.0.DF.cif
---
::
diff --git a/content/3.defense-systems/abib.md b/content/3.defense-systems/abib.md
index 0b8fb135..ee28e8af 100644
--- a/content/3.defense-systems/abib.md
+++ b/content/3.defense-systems/abib.md
@@ -56,7 +56,7 @@ Proportion of genome encoding the AbiB system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abib/AbiB__AbiB.pdb
+ - /abib/AbiB__AbiB.cif
---
::
diff --git a/content/3.defense-systems/abic.md b/content/3.defense-systems/abic.md
index f0ad4e3f..fb8584d5 100644
--- a/content/3.defense-systems/abic.md
+++ b/content/3.defense-systems/abic.md
@@ -47,7 +47,7 @@ Proportion of genome encoding the AbiC system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abic/AbiC__AbiC.pdb
+ - /abic/AbiC__AbiC.cif
---
::
diff --git a/content/3.defense-systems/abid.md b/content/3.defense-systems/abid.md
index 69670658..6b581d30 100644
--- a/content/3.defense-systems/abid.md
+++ b/content/3.defense-systems/abid.md
@@ -47,7 +47,7 @@ Proportion of genome encoding the AbiD system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abid/AbiD__AbiD.pdb
+ - /abid/AbiD__AbiD.cif
---
::
diff --git a/content/3.defense-systems/abie.md b/content/3.defense-systems/abie.md
index a7e06053..a78e824c 100644
--- a/content/3.defense-systems/abie.md
+++ b/content/3.defense-systems/abie.md
@@ -57,8 +57,8 @@ Proportion of genome encoding the AbiE system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abie/AbiE.AbiE__AbiEi.0.V.pdb
- - /abie/AbiE.AbiE__AbiEii.0.V.pdb
+ - /abie/AbiE.AbiE__AbiEi.0.V.cif
+ - /abie/AbiE.AbiE__AbiEii.0.V.cif
---
::
diff --git a/content/3.defense-systems/abig.md b/content/3.defense-systems/abig.md
index f41b6ac6..405e161c 100644
--- a/content/3.defense-systems/abig.md
+++ b/content/3.defense-systems/abig.md
@@ -47,8 +47,8 @@ Proportion of genome encoding the AbiG system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abig/AbiG.AbiG__AbiGi.0.V.pdb
- - /abig/AbiG.AbiG__AbiGii.0.V.pdb
+ - /abig/AbiG.AbiG__AbiGi.0.V.cif
+ - /abig/AbiG.AbiG__AbiGii.0.V.cif
---
::
diff --git a/content/3.defense-systems/abih.md b/content/3.defense-systems/abih.md
index 7b937eff..b895ad49 100644
--- a/content/3.defense-systems/abih.md
+++ b/content/3.defense-systems/abih.md
@@ -55,7 +55,7 @@ Proportion of genome encoding the AbiH system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abih/AbiH__AbiH.pdb
+ - /abih/AbiH__AbiH.cif
---
::
diff --git a/content/3.defense-systems/abii.md b/content/3.defense-systems/abii.md
index e2349fd4..71656679 100644
--- a/content/3.defense-systems/abii.md
+++ b/content/3.defense-systems/abii.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the AbiI system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abii/AbiI__AbiI.pdb
+ - /abii/AbiI__AbiI.cif
---
::
diff --git a/content/3.defense-systems/abij.md b/content/3.defense-systems/abij.md
index 46b1b9cc..65a2c263 100644
--- a/content/3.defense-systems/abij.md
+++ b/content/3.defense-systems/abij.md
@@ -46,7 +46,7 @@ Proportion of genome encoding the AbiJ system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abij/AbiJ__AbiJ.pdb
+ - /abij/AbiJ__AbiJ.cif
---
::
diff --git a/content/3.defense-systems/abik.md b/content/3.defense-systems/abik.md
index 5be8a8ce..52e54fcc 100644
--- a/content/3.defense-systems/abik.md
+++ b/content/3.defense-systems/abik.md
@@ -47,7 +47,7 @@ Proportion of genome encoding the AbiK system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abik/AbiK__AbiK.pdb
+ - /abik/AbiK__AbiK.cif
---
::
diff --git a/content/3.defense-systems/abil.md b/content/3.defense-systems/abil.md
index c7bc8f34..eae76d7a 100644
--- a/content/3.defense-systems/abil.md
+++ b/content/3.defense-systems/abil.md
@@ -58,8 +58,8 @@ Proportion of genome encoding the AbiL system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abil/AbiL.AbiL__AbiLi.0.V.pdb
- - /abil/AbiL.AbiL__AbiLii.0.V.pdb
+ - /abil/AbiL.AbiL__AbiLi.0.V.cif
+ - /abil/AbiL.AbiL__AbiLii.0.V.cif
---
::
diff --git a/content/3.defense-systems/abin.md b/content/3.defense-systems/abin.md
index 3eb41769..35fd7e7e 100644
--- a/content/3.defense-systems/abin.md
+++ b/content/3.defense-systems/abin.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the AbiN system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abin/AbiN__AbiN.pdb
+ - /abin/AbiN__AbiN.cif
---
::
diff --git a/content/3.defense-systems/abio.md b/content/3.defense-systems/abio.md
index 5392e139..81bacf06 100644
--- a/content/3.defense-systems/abio.md
+++ b/content/3.defense-systems/abio.md
@@ -46,7 +46,7 @@ Proportion of genome encoding the AbiO system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abio/AbiO__AbiO.pdb
+ - /abio/AbiO__AbiO.cif
---
::
diff --git a/content/3.defense-systems/abip2.md b/content/3.defense-systems/abip2.md
index e031cc40..4ee71cab 100644
--- a/content/3.defense-systems/abip2.md
+++ b/content/3.defense-systems/abip2.md
@@ -47,7 +47,7 @@ Proportion of genome encoding the AbiP2 system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /abip2/AbiP2__AbiP2.pdb
+ - /abip2/AbiP2__AbiP2.cif
---
::
diff --git a/content/3.defense-systems/abiq.md b/content/3.defense-systems/abiq.md
index 361f32e1..c322ca51 100644
--- a/content/3.defense-systems/abiq.md
+++ b/content/3.defense-systems/abiq.md
@@ -47,7 +47,7 @@ Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abiq/AbiQ__AbiQ.pdb
+ - /abiq/AbiQ__AbiQ.cif
---
::
diff --git a/content/3.defense-systems/abir.md b/content/3.defense-systems/abir.md
index 277c7ef9..3bb99407 100644
--- a/content/3.defense-systems/abir.md
+++ b/content/3.defense-systems/abir.md
@@ -46,9 +46,9 @@ Proportion of genome encoding the AbiR system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abir/AbiR.AbiR__AbiRc.0.V.pdb
- - /abir/AbiR.AbiR__AbiRb.0.V.pdb
- - /abir/AbiR.AbiR__AbiRa.0.V.pdb
+ - /abir/AbiR.AbiR__AbiRc.0.V.cif
+ - /abir/AbiR.AbiR__AbiRb.0.V.cif
+ - /abir/AbiR.AbiR__AbiRa.0.V.cif
---
::
diff --git a/content/3.defense-systems/abit.md b/content/3.defense-systems/abit.md
index 4e4e2d8d..f8456d7b 100644
--- a/content/3.defense-systems/abit.md
+++ b/content/3.defense-systems/abit.md
@@ -46,8 +46,8 @@ Proportion of genome encoding the AbiT system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abit/AbiT.AbiT__AbiTi.0.V.pdb
- - /abit/AbiT.AbiT__AbiTii.0.V.pdb
+ - /abit/AbiT.AbiT__AbiTi.0.V.cif
+ - /abit/AbiT.AbiT__AbiTii.0.V.cif
---
::
diff --git a/content/3.defense-systems/abiu.md b/content/3.defense-systems/abiu.md
index d8b3722b..b82a40a2 100644
--- a/content/3.defense-systems/abiu.md
+++ b/content/3.defense-systems/abiu.md
@@ -56,7 +56,7 @@ Proportion of genome encoding the AbiU system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abiu/AbiU__AbiU.pdb
+ - /abiu/AbiU__AbiU.cif
---
::
diff --git a/content/3.defense-systems/abiv.md b/content/3.defense-systems/abiv.md
index 89e356c4..7cfbeab8 100644
--- a/content/3.defense-systems/abiv.md
+++ b/content/3.defense-systems/abiv.md
@@ -46,7 +46,7 @@ Proportion of genome encoding the AbiV system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abiv/AbiV__AbiV.pdb
+ - /abiv/AbiV__AbiV.cif
---
::
diff --git a/content/3.defense-systems/abiz.md b/content/3.defense-systems/abiz.md
index 68931ced..50555aa0 100644
--- a/content/3.defense-systems/abiz.md
+++ b/content/3.defense-systems/abiz.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the AbiZ system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /abiz/AbiZ__AbiZ.pdb
+ - /abiz/AbiZ__AbiZ.cif
---
::
diff --git a/content/3.defense-systems/aditi.md b/content/3.defense-systems/aditi.md
index 5e539a1f..c190d06c 100644
--- a/content/3.defense-systems/aditi.md
+++ b/content/3.defense-systems/aditi.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the Aditi system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /aditi/Aditi.Aditi__DitB.0.V.pdb
- - /aditi/Aditi.Aditi__DitA.0.V.pdb
+ - /aditi/Aditi.Aditi__DitB.0.V.cif
+ - /aditi/Aditi.Aditi__DitA.0.V.cif
---
::
diff --git a/content/3.defense-systems/avs.md b/content/3.defense-systems/avs.md
index ceed5067..24396885 100644
--- a/content/3.defense-systems/avs.md
+++ b/content/3.defense-systems/avs.md
@@ -74,9 +74,9 @@ Proportion of genome encoding the Avs system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /avs/AVAST_I.AVAST_I__Avs1A.0.V.pdb
- - /avs/AVAST_I.AVAST_I__Avs1C.0.V.pdb
- - /avs/AVAST_I.AVAST_I__Avs1B.0.V.pdb
+ - /avs/AVAST_I.AVAST_I__Avs1A.0.V.cif
+ - /avs/AVAST_I.AVAST_I__Avs1C.0.V.cif
+ - /avs/AVAST_I.AVAST_I__Avs1B.0.V.cif
---
::
@@ -87,7 +87,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /avs/AVAST_II__Avs2A.pdb
+ - /avs/AVAST_II__Avs2A.cif
---
::
@@ -98,8 +98,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /avs/AVAST_III.AVAST_III__Avs3B.0.V.pdb
- - /avs/AVAST_III.AVAST_III__Avs3A.0.V.pdb
+ - /avs/AVAST_III.AVAST_III__Avs3B.0.V.cif
+ - /avs/AVAST_III.AVAST_III__Avs3A.0.V.cif
---
::
@@ -110,7 +110,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /avs/AVAST_IV__Avs4A.pdb
+ - /avs/AVAST_IV__Avs4A.cif
---
::
@@ -121,7 +121,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /avs/AVAST_V__Avs5A.pdb
+ - /avs/AVAST_V__Avs5A.cif
---
::
diff --git a/content/3.defense-systems/azaca.md b/content/3.defense-systems/azaca.md
index 50ea7855..3b7206d9 100644
--- a/content/3.defense-systems/azaca.md
+++ b/content/3.defense-systems/azaca.md
@@ -45,9 +45,9 @@ Proportion of genome encoding the Azaca system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /azaca/Azaca.Azaca__ZacA.0.V.pdb
- - /azaca/Azaca.Azaca__ZacB.0.V.pdb
- - /azaca/Azaca.Azaca__ZacC.0.V.pdb
+ - /azaca/Azaca.Azaca__ZacA.0.V.cif
+ - /azaca/Azaca.Azaca__ZacB.0.V.cif
+ - /azaca/Azaca.Azaca__ZacC.0.V.cif
---
::
diff --git a/content/3.defense-systems/borvo.md b/content/3.defense-systems/borvo.md
index 457341c1..9a733dd6 100644
--- a/content/3.defense-systems/borvo.md
+++ b/content/3.defense-systems/borvo.md
@@ -57,7 +57,7 @@ Proportion of genome encoding the Borvo system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /borvo/Borvo__BovA.pdb
+ - /borvo/Borvo__BovA.cif
---
::
diff --git a/content/3.defense-systems/brex.md b/content/3.defense-systems/brex.md
index 7b3a1e2b..e1f96037 100644
--- a/content/3.defense-systems/brex.md
+++ b/content/3.defense-systems/brex.md
@@ -93,11 +93,11 @@ Proportion of genome encoding the BREX system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /brex/BREX_VI.BREX__brxHI.0.DF.pdb
- - /brex/BREX_VI.BREX__brxD.0.DF.pdb
- - /brex/BREX_II.BREX__pglY.0.DF.pdb
- - /brex/BREX_II.BREX__pglX2.0.DF.pdb
- - /brex/BREX_II.BREX__pglW.0.DF.pdb
+ - /brex/BREX_VI.BREX__brxHI.0.DF.cif
+ - /brex/BREX_VI.BREX__brxD.0.DF.cif
+ - /brex/BREX_II.BREX__pglY.0.DF.cif
+ - /brex/BREX_II.BREX__pglX2.0.DF.cif
+ - /brex/BREX_II.BREX__pglW.0.DF.cif
---
::
@@ -108,11 +108,11 @@ dataUrls:
---
height: 700
dataUrls:
- - /brex/BREX_III.BREX__brxF.0.DF.pdb
- - /brex/BREX_III.BREX__pglXI.0.DF.pdb
- - /brex/BREX_V.BREX__brxHII.0.DF.pdb
- - /brex/BREX_III.BREX__pglZ3.0.DF.pdb
- - /brex/BREX_III.BREX__brxA.0.DF.pdb
+ - /brex/BREX_III.BREX__brxF.0.DF.cif
+ - /brex/BREX_III.BREX__pglXI.0.DF.cif
+ - /brex/BREX_V.BREX__brxHII.0.DF.cif
+ - /brex/BREX_III.BREX__pglZ3.0.DF.cif
+ - /brex/BREX_III.BREX__brxA.0.DF.cif
---
::
@@ -123,8 +123,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /brex/BREX_IV.BREX__brxP.0.DF.pdb
- - /brex/BREX_IV.BREX__PglZ.0.DF.pdb
+ - /brex/BREX_IV.BREX__brxP.0.DF.cif
+ - /brex/BREX_IV.BREX__PglZ.0.DF.cif
---
::
@@ -135,8 +135,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /brex/BREX_V.BREX__brxHII.0.DF.pdb
- - /brex/BREX_VI.BREX__pglZA.0.DF.pdb
+ - /brex/BREX_V.BREX__brxHII.0.DF.cif
+ - /brex/BREX_VI.BREX__pglZA.0.DF.cif
---
::
@@ -147,11 +147,11 @@ dataUrls:
---
height: 700
dataUrls:
- - /brex/BREX_VI.BREX__brxHI.0.DF.pdb
- - /brex/BREX_VI.BREX__brxD.0.DF.pdb
- - /brex/BREX_VI.BREX__pglZA.0.DF.pdb
- - /brex/BREX_VI.BREX_brxA.0.DF.pdb
- - /brex/BREX_VI.BREX__brxE.0.DF.pdb
+ - /brex/BREX_VI.BREX__brxHI.0.DF.cif
+ - /brex/BREX_VI.BREX__brxD.0.DF.cif
+ - /brex/BREX_VI.BREX__pglZA.0.DF.cif
+ - /brex/BREX_VI.BREX_brxA.0.DF.cif
+ - /brex/BREX_VI.BREX__brxE.0.DF.cif
---
::
diff --git a/content/3.defense-systems/bsta.md b/content/3.defense-systems/bsta.md
index 882b9ead..023957a9 100644
--- a/content/3.defense-systems/bsta.md
+++ b/content/3.defense-systems/bsta.md
@@ -54,9 +54,9 @@ Proportion of genome encoding the BstA system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /bsta/BstA__BstA.pdb
- - /bsta/BstA__BstA1.pdb
- - /bsta/BstA__BstA2.pdb
+ - /bsta/BstA__BstA.cif
+ - /bsta/BstA__BstA1.cif
+ - /bsta/BstA__BstA2.cif
---
::
diff --git a/content/3.defense-systems/bunzi.md b/content/3.defense-systems/bunzi.md
index 95b0915b..bb4e378c 100644
--- a/content/3.defense-systems/bunzi.md
+++ b/content/3.defense-systems/bunzi.md
@@ -54,8 +54,8 @@ Proportion of genome encoding the Bunzi system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /bunzi/Bunzi.Bunzi__BnzB.0.V.pdb
- - /bunzi/Bunzi.Bunzi__BnzA.0.V.pdb
+ - /bunzi/Bunzi.Bunzi__BnzB.0.V.cif
+ - /bunzi/Bunzi.Bunzi__BnzA.0.V.cif
---
::
diff --git a/content/3.defense-systems/butters_gp30_gp31.md b/content/3.defense-systems/butters_gp30_gp31.md
index 9dccad03..6295e2b6 100644
--- a/content/3.defense-systems/butters_gp30_gp31.md
+++ b/content/3.defense-systems/butters_gp30_gp31.md
@@ -66,8 +66,8 @@ Proportion of genome encoding the Butters_gp30_gp31 system for the 14 phyla with
---
height: 700
dataUrls:
- - /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp30.pdb
- - /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp31.pdb
+ - /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp30.cif
+ - /butters_gp30_gp31/Butters_gp30_gp31__Butters_gp31.cif
---
::
diff --git a/content/3.defense-systems/butters_gp57r.md b/content/3.defense-systems/butters_gp57r.md
index 4efd9095..829d15af 100644
--- a/content/3.defense-systems/butters_gp57r.md
+++ b/content/3.defense-systems/butters_gp57r.md
@@ -44,7 +44,7 @@ Proportion of genome encoding the Butters_gp57r system for the 14 phyla with mor
---
height: 700
dataUrls:
- - /butters_gp57r/Butters_gp57r__gp57r.pdb
+ - /butters_gp57r/Butters_gp57r__gp57r.cif
---
::
diff --git a/content/3.defense-systems/caprel.md b/content/3.defense-systems/caprel.md
index 2abb480e..fe8b2e44 100644
--- a/content/3.defense-systems/caprel.md
+++ b/content/3.defense-systems/caprel.md
@@ -57,7 +57,7 @@ Proportion of genome encoding the CapRel system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /caprel/CapRel__CapRel.pdb
+ - /caprel/CapRel__CapRel.cif
---
::
diff --git a/content/3.defense-systems/cas.md b/content/3.defense-systems/cas.md
index 665e5b5c..70fed3ee 100644
--- a/content/3.defense-systems/cas.md
+++ b/content/3.defense-systems/cas.md
@@ -1,55 +1,55 @@
----
-title: CRISPR-Cas
-layout: article
-tableColumns:
- article:
- doi: 10.1038/nrmicro3569
- abstract: |
- The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
----
-
-# CRISPR-Cas
-
-For the CRISPR-Cas system, a good place to start is the [Wikipedia page](https://en.wikipedia.org/wiki/CRISPR)
-
-## Example of genomic structure
-
-CRISPR-Cas systems have been classified in 6 different families :ref{doi=10.1038/s41579-019-0299-x}.
-Each family is composed of different subtypes. For example, Type I CRISPR is composed of 7 subtypes: I-A to I-G.
-
-Here is example of each of the 6 family found in the RefSeq database:
-
-{max-width=750px}
-
-The CAS_Class1-Subtype-I-E system in *Citrobacter sp. RHBSTW-00017* (GCF_013797615.1, NZ_CP056899) is composed of 8 proteins cas3_I_5 (WP_103284157.1) cas8e_I-E_1 (HV037_RS05730) cse2gr11_I-E_2 (HV037_RS05735) cas7_I-E_2 (HV037_RS05740) cas5_I-E_3 (HV037_RS05745) cas6e_I_II_III_IV_V_VI_1 (HV037_RS05750) cas1_I-E_1 (HV037_RS05755) cas2_I-E_2 (HV037_RS05760)
-
-{max-width=750px}
-
-The CAS_Class2-Subtype-II-A system in *Streptococcus agalactiae* (GCF_001190885.1, NZ_CP011329) is composed of 4 proteins cas9_II-A_II-B_II-C_3 (SAH002_RS04760) cas1_I_II_III_IV_V_VI_5 (SAH002_RS04765) cas2_I_II_III_IV_V_VI_6 (SAH002_RS04770) csn2_II-A_4 (SAH002_RS04775)
-
-{max-width=750px}
-
-The CAS_Class1-Subtype-III-A system in *Mycobacterium tuberculosis* (GCF_014900005.1, NZ_CP041828) is composed of 9 proteins cas2_I_II_III_IV_V_VI_5 (FPJ80_RS14760) cas1_I_II_III_IV_V_VI_8 (FPJ80_RS14765) csm6_III_2 (FPJ80_RS14770) csm5gr7_III-A_3 (FPJ80_RS14775) csm4gr5_III-A_3 (FPJ80_RS14780) csm3gr7_III-A_1 (FPJ80_RS14785) csm2gr11_III-A_1 (FPJ80_RS14790) cas10_III_7 (FPJ80_RS14795) cas6_I_II_III_IV_V_VI_15 (FPJ80_RS14800)
-
-{max-width=750px}
-
-The CAS_Class1-Subtype-IV-A system in *Shigella flexneri* (GCF_022353685.1, NZ_CP054978) is composed of 5 proteins csf1gr8_IV-A_3 (WP_038989757.1) cas6e_I_II_III_IV_V_VI_3 (WP_038989755.1) csf4_IV-A_1 (WP_016947078.1) csf3gr5_IV-A_1 (WP_004181864.1) csf2gr7_IV-A_1 (WP_029505552.1)
-
-
-{max-width=750px}
-
-The CAS_Class2-Subtype-V-A system in *Francisella tularensis* (GCF_001865695.1, NZ_CP016635) is composed of 4 proteins cas2_I_II_III_IV_V_VI_3 (N894_RS07580) cas1_I_II_III_IV_V_VI_1 (N894_RS07585) cas4_V_1 (N894_RS07590) cas12a_V-A_4 (N894_RS07595)
-
-{max-width=750px}
-
-The CAS_Class2-Subtype-VI-A system in *Leptotrichia shahii* (GCF_008327825.1, NZ_AP019827) is composed of 3 proteins cas13a_VI-A_1 (F1564_RS00570) cas1_I_II_III_IV_V_VI_5 (F1564_RS00575) cas2_I_II_III_IV_V_VI_11 (F1564_RS00580)
-
-## Distribution of the system among prokaryotes
-
-Among the 22,803 complete genomes of RefSeq, the AbiC is detected in 8581 genomes (37.63 %).
-
-The system was detected in 2905 different species.
-
-{max-width=750px}
-
-Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.
+---
+title: CRISPR-Cas
+layout: article
+tableColumns:
+ article:
+ doi: 10.1038/nrmicro3569
+ abstract: |
+ The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
+---
+
+# CRISPR-Cas
+
+For the CRISPR-Cas system, a good place to start is the [Wikipedia page](https://en.wikipedia.org/wiki/CRISPR)
+
+## Example of genomic structure
+
+CRISPR-Cas systems have been classified in 6 different families :ref{doi=10.1038/s41579-019-0299-x}.
+Each family is composed of different subtypes. For example, Type I CRISPR is composed of 7 subtypes: I-A to I-G.
+
+Here is example of each of the 6 family found in the RefSeq database:
+
+{max-width=750px}
+
+The CAS_Class1-Subtype-I-E system in *Citrobacter sp. RHBSTW-00017* (GCF_013797615.1, NZ_CP056899) is composed of 8 proteins cas3_I_5 (WP_103284157.1) cas8e_I-E_1 (HV037_RS05730) cse2gr11_I-E_2 (HV037_RS05735) cas7_I-E_2 (HV037_RS05740) cas5_I-E_3 (HV037_RS05745) cas6e_I_II_III_IV_V_VI_1 (HV037_RS05750) cas1_I-E_1 (HV037_RS05755) cas2_I-E_2 (HV037_RS05760)
+
+{max-width=750px}
+
+The CAS_Class2-Subtype-II-A system in *Streptococcus agalactiae* (GCF_001190885.1, NZ_CP011329) is composed of 4 proteins cas9_II-A_II-B_II-C_3 (SAH002_RS04760) cas1_I_II_III_IV_V_VI_5 (SAH002_RS04765) cas2_I_II_III_IV_V_VI_6 (SAH002_RS04770) csn2_II-A_4 (SAH002_RS04775)
+
+{max-width=750px}
+
+The CAS_Class1-Subtype-III-A system in *Mycobacterium tuberculosis* (GCF_014900005.1, NZ_CP041828) is composed of 9 proteins cas2_I_II_III_IV_V_VI_5 (FPJ80_RS14760) cas1_I_II_III_IV_V_VI_8 (FPJ80_RS14765) csm6_III_2 (FPJ80_RS14770) csm5gr7_III-A_3 (FPJ80_RS14775) csm4gr5_III-A_3 (FPJ80_RS14780) csm3gr7_III-A_1 (FPJ80_RS14785) csm2gr11_III-A_1 (FPJ80_RS14790) cas10_III_7 (FPJ80_RS14795) cas6_I_II_III_IV_V_VI_15 (FPJ80_RS14800)
+
+{max-width=750px}
+
+The CAS_Class1-Subtype-IV-A system in *Shigella flexneri* (GCF_022353685.1, NZ_CP054978) is composed of 5 proteins csf1gr8_IV-A_3 (WP_038989757.1) cas6e_I_II_III_IV_V_VI_3 (WP_038989755.1) csf4_IV-A_1 (WP_016947078.1) csf3gr5_IV-A_1 (WP_004181864.1) csf2gr7_IV-A_1 (WP_029505552.1)
+
+
+{max-width=750px}
+
+The CAS_Class2-Subtype-V-A system in *Francisella tularensis* (GCF_001865695.1, NZ_CP016635) is composed of 4 proteins cas2_I_II_III_IV_V_VI_3 (N894_RS07580) cas1_I_II_III_IV_V_VI_1 (N894_RS07585) cas4_V_1 (N894_RS07590) cas12a_V-A_4 (N894_RS07595)
+
+{max-width=750px}
+
+The CAS_Class2-Subtype-VI-A system in *Leptotrichia shahii* (GCF_008327825.1, NZ_AP019827) is composed of 3 proteins cas13a_VI-A_1 (F1564_RS00570) cas1_I_II_III_IV_V_VI_5 (F1564_RS00575) cas2_I_II_III_IV_V_VI_11 (F1564_RS00580)
+
+## Distribution of the system among prokaryotes
+
+Among the 22,803 complete genomes of RefSeq, the AbiC is detected in 8581 genomes (37.63 %).
+
+The system was detected in 2905 different species.
+
+{max-width=750px}
+
+Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.
diff --git a/content/3.defense-systems/cbass.md b/content/3.defense-systems/cbass.md
index 029e52c7..781d10e9 100644
--- a/content/3.defense-systems/cbass.md
+++ b/content/3.defense-systems/cbass.md
@@ -62,8 +62,8 @@ Proportion of genome encoding the CBASS system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.pdb
- - /cbass/CBASS_I.CBASS__TM.0.V.pdb
+ - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.cif
+ - /cbass/CBASS_I.CBASS__TM.0.V.cif
---
::
@@ -74,10 +74,10 @@ dataUrls:
---
height: 700
dataUrls:
- - /cbass/CBASS_II.CBASS__Phospholipase.0.V.pdb
- - /cbass/CBASS_II.CBASS__AG_E2_Prok-E2.0.V.pdb
- - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.pdb
- - /cbass/CBASS_II.CBASS__Jab.0.V.pdb
+ - /cbass/CBASS_II.CBASS__Phospholipase.0.V.cif
+ - /cbass/CBASS_II.CBASS__AG_E2_Prok-E2.0.V.cif
+ - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.cif
+ - /cbass/CBASS_II.CBASS__Jab.0.V.cif
---
::
@@ -88,11 +88,11 @@ dataUrls:
---
height: 700
dataUrls:
- - /cbass/CBASS_III.CBASS__Endonuc_small.0.V.pdb
- - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.pdb
- - /cbass/CBASS_III.CBASS__bacHORMA_2.0.V.pdb
- - /cbass/CBASS_III.CBASS__HORMA.0.V.pdb
- - /cbass/CBASS_III.CBASS__TRIP13.0.V.pdb
+ - /cbass/CBASS_III.CBASS__Endonuc_small.0.V.cif
+ - /cbass/CBASS_I.CBASS__Cyclase_II.0.V.cif
+ - /cbass/CBASS_III.CBASS__bacHORMA_2.0.V.cif
+ - /cbass/CBASS_III.CBASS__HORMA.0.V.cif
+ - /cbass/CBASS_III.CBASS__TRIP13.0.V.cif
---
::
@@ -103,11 +103,11 @@ dataUrls:
---
height: 700
dataUrls:
- - /cbass/CBASS_IV.CBASS__QueC.0.DF.pdb
- - /cbass/CBASS_IV.CBASS__TGT.0.DF.pdb
- - /cbass/CBASS_IV.CBASS__Cyclase_SMODS.0.DF.pdb
- - /cbass/CBASS_IV.CBASS__2TM_type_IV.0.DF.pdb
- - /cbass/CBASS_IV.CBASS__OGG.0.DF.pdb
+ - /cbass/CBASS_IV.CBASS__QueC.0.DF.cif
+ - /cbass/CBASS_IV.CBASS__TGT.0.DF.cif
+ - /cbass/CBASS_IV.CBASS__Cyclase_SMODS.0.DF.cif
+ - /cbass/CBASS_IV.CBASS__2TM_type_IV.0.DF.cif
+ - /cbass/CBASS_IV.CBASS__OGG.0.DF.cif
---
::
diff --git a/content/3.defense-systems/charlie_gp32.md b/content/3.defense-systems/charlie_gp32.md
index 9c39da40..98e6d5c7 100644
--- a/content/3.defense-systems/charlie_gp32.md
+++ b/content/3.defense-systems/charlie_gp32.md
@@ -44,7 +44,7 @@ Proportion of genome encoding the Charlie_gp32 system for the 14 phyla with more
---
height: 700
dataUrls:
- - /charlie_gp32/Charlie_gp32__gp32.pdb
+ - /charlie_gp32/Charlie_gp32__gp32.cif
---
::
diff --git a/content/3.defense-systems/dartg.md b/content/3.defense-systems/dartg.md
index 7b8a0e29..188564c3 100644
--- a/content/3.defense-systems/dartg.md
+++ b/content/3.defense-systems/dartg.md
@@ -59,8 +59,8 @@ Proportion of genome encoding the DarTG system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /dartg/DarTG.DarTG_DarT.0.DF.pdb
- - /dartg/DarTG.DarTG_DarG.0.DF.pdb
+ - /dartg/DarTG.DarTG_DarT.0.DF.cif
+ - /dartg/DarTG.DarTG_DarG.0.DF.cif
---
::
diff --git a/content/3.defense-systems/dazbog.md b/content/3.defense-systems/dazbog.md
index 6060fa8f..2f47c1a0 100644
--- a/content/3.defense-systems/dazbog.md
+++ b/content/3.defense-systems/dazbog.md
@@ -54,8 +54,8 @@ Proportion of genome encoding the Dazbog system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /dazbog/Dazbog.Dazbog__DzbA.1.V.pdb
- - /dazbog/Dazbog.Dazbog__DzbB.1.V.pdb
+ - /dazbog/Dazbog.Dazbog__DzbA.1.V.cif
+ - /dazbog/Dazbog.Dazbog__DzbB.1.V.cif
---
::
@@ -65,8 +65,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /dazbog/Dazbog.Dazbog__DzbA.1.V.pdb
- - /dazbog/Dazbog.Dazbog__DzbB.1.V.pdb
+ - /dazbog/Dazbog.Dazbog__DzbA.1.V.cif
+ - /dazbog/Dazbog.Dazbog__DzbB.1.V.cif
---
::
diff --git a/content/3.defense-systems/dctpdeaminase.md b/content/3.defense-systems/dctpdeaminase.md
index 4f0235f7..9deca9d9 100644
--- a/content/3.defense-systems/dctpdeaminase.md
+++ b/content/3.defense-systems/dctpdeaminase.md
@@ -59,7 +59,7 @@ Proportion of genome encoding the dCTPdeaminase system for the 14 phyla with mor
---
height: 700
dataUrls:
- - /dctpdeaminase/dCTPdeaminase__dCTPdeaminase.pdb
+ - /dctpdeaminase/dCTPdeaminase__dCTPdeaminase.cif
---
::
diff --git a/content/3.defense-systems/ddmde.md b/content/3.defense-systems/ddmde.md
index 2e3c30ec..37075254 100644
--- a/content/3.defense-systems/ddmde.md
+++ b/content/3.defense-systems/ddmde.md
@@ -41,8 +41,8 @@ Proportion of genome encoding the DdmDE system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /ddmde/DdmDE.DdmDE__DdmD.0.V.pdb
- - /ddmde/DdmDE.DdmDE__DdmE.0.V.pdb
+ - /ddmde/DdmDE.DdmDE__DdmD.0.V.cif
+ - /ddmde/DdmDE.DdmDE__DdmE.0.V.cif
---
::
diff --git a/content/3.defense-systems/detocs.md b/content/3.defense-systems/detocs.md
index 3ddb8843..fcbbaf0e 100644
--- a/content/3.defense-systems/detocs.md
+++ b/content/3.defense-systems/detocs.md
@@ -74,9 +74,9 @@ Proportion of genome encoding the Detocs system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /detocs/Detocs__dtcC.pdb
- - /detocs/Detocs__dtcB.pdb
- - /detocs/Detocs__dtcA.pdb
+ - /detocs/Detocs__dtcC.cif
+ - /detocs/Detocs__dtcB.cif
+ - /detocs/Detocs__dtcA.cif
---
::
@@ -87,9 +87,9 @@ dataUrls:
---
height: 700
dataUrls:
- - /detocs/Detocs_hydrolase__dtcC.pdb
- - /detocs/Detocs_hydrolase__dtcB.pdb
- - /detocs/Detocs_hydrolase__dtcA.pdb
+ - /detocs/Detocs_hydrolase__dtcC.cif
+ - /detocs/Detocs_hydrolase__dtcB.cif
+ - /detocs/Detocs_hydrolase__dtcA.cif
---
::
diff --git a/content/3.defense-systems/dgtpase.md b/content/3.defense-systems/dgtpase.md
index 55ce9aaf..d88cd781 100644
--- a/content/3.defense-systems/dgtpase.md
+++ b/content/3.defense-systems/dgtpase.md
@@ -54,7 +54,7 @@ Proportion of genome encoding the dGTPase system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /dgtpase/dGTPase__Sp_dGTPase.pdb
+ - /dgtpase/dGTPase__Sp_dGTPase.cif
---
::
diff --git a/content/3.defense-systems/disarm.md b/content/3.defense-systems/disarm.md
index 100fac7a..690bad66 100644
--- a/content/3.defense-systems/disarm.md
+++ b/content/3.defense-systems/disarm.md
@@ -70,11 +70,11 @@ Proportion of genome encoding the DISARM system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /disarm/DISARM_2.DISARM__drmC.0.V.pdb
- - /disarm/DISARM_2.DISARM__drmB.0.V.pdb
- - /disarm/DISARM_1.DISARM__drmA.0.DF.pdb
- - /disarm/DISARM_1.DISARM_1__drmMI.0.DF.pdb
- - /disarm/DISARM_1.DISARM_1__drmD.0.DF.pdb
+ - /disarm/DISARM_2.DISARM__drmC.0.V.cif
+ - /disarm/DISARM_2.DISARM__drmB.0.V.cif
+ - /disarm/DISARM_1.DISARM__drmA.0.DF.cif
+ - /disarm/DISARM_1.DISARM_1__drmMI.0.DF.cif
+ - /disarm/DISARM_1.DISARM_1__drmD.0.DF.cif
---
::
@@ -85,11 +85,11 @@ dataUrls:
---
height: 700
dataUrls:
- - /disarm/DISARM_1.DISARM__drmA.0.DF.pdb
- - /disarm/DISARM_2.DISARM__drmC.0.V.pdb
- - /disarm/DISARM_2.DISARM_2__drmMII.0.V.pdb
- - /disarm/DISARM_2.DISARM__drmB.0.V.pdb
- - /disarm/DISARM_2.DISARM_2__drmE.0.V.pdb
+ - /disarm/DISARM_1.DISARM__drmA.0.DF.cif
+ - /disarm/DISARM_2.DISARM__drmC.0.V.cif
+ - /disarm/DISARM_2.DISARM_2__drmMII.0.V.cif
+ - /disarm/DISARM_2.DISARM__drmB.0.V.cif
+ - /disarm/DISARM_2.DISARM_2__drmE.0.V.cif
---
::
diff --git a/content/3.defense-systems/dnd.md b/content/3.defense-systems/dnd.md
index 7319afe1..0dd0b921 100644
--- a/content/3.defense-systems/dnd.md
+++ b/content/3.defense-systems/dnd.md
@@ -50,12 +50,12 @@ Proportion of genome encoding the Dnd system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.pdb
- - /dnd/Dnd_ABCDE.Dnd__DndE.0.DF.pdb
- - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.pdb
- - /dnd/Dnd_ABCDE.Dnd__DndC.0.DF.pdb
- - /dnd/Dnd_ABCDEFGH.Dnd__DndB.0.DF.pdb
- - /dnd/Dnd_ABCDE.Dnd__DndA.0.DF.pdb
+ - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.cif
+ - /dnd/Dnd_ABCDE.Dnd__DndE.0.DF.cif
+ - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.cif
+ - /dnd/Dnd_ABCDE.Dnd__DndC.0.DF.cif
+ - /dnd/Dnd_ABCDEFGH.Dnd__DndB.0.DF.cif
+ - /dnd/Dnd_ABCDE.Dnd__DndA.0.DF.cif
---
::
@@ -66,14 +66,14 @@ dataUrls:
---
height: 700
dataUrls:
- - /dnd/Dnd_ABCDE.Dnd__DndA.0.DF.pdb
- - /dnd/Dnd_ABCDEFGH.Dnd__DndB.0.DF.pdb
- - /dnd/Dnd_ABCDE.Dnd__DndC.0.DF.pdb
- - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.pdb
- - /dnd/Dnd_ABCDE.Dnd__DndE.0.DF.pdb
- - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptH.0.DF.pdb
- - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptG.0.DF.pdb
- - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptF.0.DF.pdb
+ - /dnd/Dnd_ABCDE.Dnd__DndA.0.DF.cif
+ - /dnd/Dnd_ABCDEFGH.Dnd__DndB.0.DF.cif
+ - /dnd/Dnd_ABCDE.Dnd__DndC.0.DF.cif
+ - /dnd/Dnd_ABCDE.Dnd__DndD.0.DF.cif
+ - /dnd/Dnd_ABCDE.Dnd__DndE.0.DF.cif
+ - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptH.0.DF.cif
+ - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptG.0.DF.cif
+ - /dnd/Dnd_ABCDEFGH.Dnd_ABCDEFGH__DptF.0.DF.cif
---
::
diff --git a/content/3.defense-systems/dodola.md b/content/3.defense-systems/dodola.md
index a7c02de8..fa8cda44 100644
--- a/content/3.defense-systems/dodola.md
+++ b/content/3.defense-systems/dodola.md
@@ -56,8 +56,8 @@ Proportion of genome encoding the Dodola system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /dodola/Dodola.Dodola__DolB.0.V.pdb
- - /dodola/Dodola.Dodola__DolA.0.V.pdb
+ - /dodola/Dodola.Dodola__DolB.0.V.cif
+ - /dodola/Dodola.Dodola__DolA.0.V.cif
---
::
diff --git a/content/3.defense-systems/dpd.md b/content/3.defense-systems/dpd.md
index 599a877b..76728977 100644
--- a/content/3.defense-systems/dpd.md
+++ b/content/3.defense-systems/dpd.md
@@ -42,18 +42,18 @@ Proportion of genome encoding the Dpd system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /dpd/Dpd.Dpd__QueD.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdD.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdK.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdJ.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdI.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdH.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdG.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdF.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdE.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdB.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdA.0.DF.pdb
- - /dpd/Dpd.Dpd__DpdC.0.DF.pdb
+ - /dpd/Dpd.Dpd__QueD.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdD.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdK.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdJ.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdI.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdH.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdG.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdF.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdE.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdB.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdA.0.DF.cif
+ - /dpd/Dpd.Dpd__DpdC.0.DF.cif
---
::
diff --git a/content/3.defense-systems/drt.md b/content/3.defense-systems/drt.md
index 20be54df..8255fad5 100644
--- a/content/3.defense-systems/drt.md
+++ b/content/3.defense-systems/drt.md
@@ -103,7 +103,7 @@ Proportion of genome encoding the DRT system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /drt/DRT6__DRT6.pdb
+ - /drt/DRT6__DRT6.cif
---
::
@@ -114,7 +114,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /drt/DRT7__DRT7.pdb
+ - /drt/DRT7__DRT7.cif
---
::
@@ -125,7 +125,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /drt/DRT8__DRT8.pdb
+ - /drt/DRT8__DRT8.cif
---
::
@@ -136,7 +136,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /drt/DRT9__DRT9.pdb
+ - /drt/DRT9__DRT9.cif
---
::
@@ -147,8 +147,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /drt/DRT_1.DRT_1__drt1b.0.V.pdb
- - /drt/DRT_1.DRT_1__drt1a.0.V.pdb
+ - /drt/DRT_1.DRT_1__drt1b.0.V.cif
+ - /drt/DRT_1.DRT_1__drt1a.0.V.cif
---
::
@@ -159,7 +159,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /drt/DRT_2__drt2.pdb
+ - /drt/DRT_2__drt2.cif
---
::
@@ -170,8 +170,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /drt/DRT_3.DRT_3__drt3b.0.V.pdb
- - /drt/DRT_3.DRT_3__drt3a.0.V.pdb
+ - /drt/DRT_3.DRT_3__drt3b.0.V.cif
+ - /drt/DRT_3.DRT_3__drt3a.0.V.cif
---
::
@@ -182,7 +182,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /drt/DRT_4__drt4.pdb
+ - /drt/DRT_4__drt4.cif
---
::
@@ -193,7 +193,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /drt/DRT_5__drt5.pdb
+ - /drt/DRT_5__drt5.cif
---
::
diff --git a/content/3.defense-systems/druantia.md b/content/3.defense-systems/druantia.md
index 3f394efe..501ad255 100644
--- a/content/3.defense-systems/druantia.md
+++ b/content/3.defense-systems/druantia.md
@@ -53,11 +53,11 @@ Proportion of genome encoding the Druantia system for the 14 phyla with more tha
---
height: 700
dataUrls:
- - /druantia/Druantia_I.Druantia_I__DruA.0.V.pdb
- - /druantia/Druantia_I.Druantia_I__DruB.0.V.pdb
- - /druantia/Druantia_I.Druantia_I__DruC.0.V.pdb
- - /druantia/Druantia_I.Druantia_I__DruD.0.V.pdb
- - /druantia/Druantia_I.Druantia__DruE.0.V.pdb
+ - /druantia/Druantia_I.Druantia_I__DruA.0.V.cif
+ - /druantia/Druantia_I.Druantia_I__DruB.0.V.cif
+ - /druantia/Druantia_I.Druantia_I__DruC.0.V.cif
+ - /druantia/Druantia_I.Druantia_I__DruD.0.V.cif
+ - /druantia/Druantia_I.Druantia__DruE.0.V.cif
---
::
@@ -68,10 +68,10 @@ dataUrls:
---
height: 700
dataUrls:
- - /druantia/Druantia_II.Druantia_II__DruM.0.DF.pdb
- - /druantia/Druantia_II.Druantia_II__DruF.0.DF.pdb
- - /druantia/Druantia_II.Druantia_II__DruG.0.DF.pdb
- - /druantia/Druantia_II.Druantia__DruE_2.0.DF.pdb
+ - /druantia/Druantia_II.Druantia_II__DruM.0.DF.cif
+ - /druantia/Druantia_II.Druantia_II__DruF.0.DF.cif
+ - /druantia/Druantia_II.Druantia_II__DruG.0.DF.cif
+ - /druantia/Druantia_II.Druantia__DruE_2.0.DF.cif
---
::
@@ -82,8 +82,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /druantia/Druantia_III.Druantia_III__DruH.0.DF.pdb
- - /druantia/Druantia_III.Druantia__DruE_3.0.DF.pdb
+ - /druantia/Druantia_III.Druantia_III__DruH.0.DF.cif
+ - /druantia/Druantia_III.Druantia__DruE_3.0.DF.cif
---
::
diff --git a/content/3.defense-systems/dsr.md b/content/3.defense-systems/dsr.md
index 12d240d9..7707a5fb 100644
--- a/content/3.defense-systems/dsr.md
+++ b/content/3.defense-systems/dsr.md
@@ -50,7 +50,7 @@ Proportion of genome encoding the Dsr system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /dsr/Dsr_I__Dsr1.pdb
+ - /dsr/Dsr_I__Dsr1.cif
---
::
@@ -61,7 +61,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /dsr/Dsr_II__Dsr2.pdb
+ - /dsr/Dsr_II__Dsr2.cif
---
::
diff --git a/content/3.defense-systems/eleos.md b/content/3.defense-systems/eleos.md
index 5370ae15..e413458c 100644
--- a/content/3.defense-systems/eleos.md
+++ b/content/3.defense-systems/eleos.md
@@ -47,8 +47,8 @@ Proportion of genome encoding the Eleos system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /eleos/Eleos.Eleos__LeoBC.0.V.pdb
- - /eleos/Eleos.Eleos__LeoA.0.V.pdb
+ - /eleos/Eleos.Eleos__LeoBC.0.V.cif
+ - /eleos/Eleos.Eleos__LeoA.0.V.cif
---
::
diff --git a/content/3.defense-systems/fs_giy_yig.md b/content/3.defense-systems/fs_giy_yig.md
index ff41e101..81904d66 100644
--- a/content/3.defense-systems/fs_giy_yig.md
+++ b/content/3.defense-systems/fs_giy_yig.md
@@ -44,7 +44,7 @@ Proportion of genome encoding the FS_GIY_YIG system for the 14 phyla with more t
---
height: 700
dataUrls:
- - /fs_giy_yig/FS_GIY_YIG__GIY_YIG.pdb
+ - /fs_giy_yig/FS_GIY_YIG__GIY_YIG.cif
---
::
diff --git a/content/3.defense-systems/fs_hepn_tm.md b/content/3.defense-systems/fs_hepn_tm.md
index 0ccac65e..14a2f2cb 100644
--- a/content/3.defense-systems/fs_hepn_tm.md
+++ b/content/3.defense-systems/fs_hepn_tm.md
@@ -23,8 +23,8 @@ relevantAbstracts:
---
height: 700
dataUrls:
- - /fs_hepn_tm/FS_HEPN_TM__TM.pdb
- - /fs_hepn_tm/FS_HEPN_TM__HEPN.pdb
+ - /fs_hepn_tm/FS_HEPN_TM__TM.cif
+ - /fs_hepn_tm/FS_HEPN_TM__HEPN.cif
---
::
diff --git a/content/3.defense-systems/fs_hp.md b/content/3.defense-systems/fs_hp.md
index e78e5658..29ae01a7 100644
--- a/content/3.defense-systems/fs_hp.md
+++ b/content/3.defense-systems/fs_hp.md
@@ -52,7 +52,7 @@ Proportion of genome encoding the FS_HP system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /fs_hp/FS_HP__HP.pdb
+ - /fs_hp/FS_HP__HP.cif
---
::
diff --git a/content/3.defense-systems/fs_hp_sdh_sah.md b/content/3.defense-systems/fs_hp_sdh_sah.md
index 5c0d6e5f..373542ed 100644
--- a/content/3.defense-systems/fs_hp_sdh_sah.md
+++ b/content/3.defense-systems/fs_hp_sdh_sah.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the FS_HP_SDH_sah system for the 14 phyla with mor
---
height: 700
dataUrls:
- - /fs_hp_sdh_sah/FS_HP_SDH_sah__SDH_sah.pdb
- - /fs_hp_sdh_sah/FS_HP_SDH_sah__HP.pdb
+ - /fs_hp_sdh_sah/FS_HP_SDH_sah__SDH_sah.cif
+ - /fs_hp_sdh_sah/FS_HP_SDH_sah__HP.cif
---
::
diff --git a/content/3.defense-systems/fs_hsdr_like.md b/content/3.defense-systems/fs_hsdr_like.md
index adaff9db..4f07aeee 100644
--- a/content/3.defense-systems/fs_hsdr_like.md
+++ b/content/3.defense-systems/fs_hsdr_like.md
@@ -44,7 +44,7 @@ Proportion of genome encoding the FS_HsdR_like system for the 14 phyla with more
---
height: 700
dataUrls:
- - /fs_hsdr_like/FS_HsdR_like_HP.pdb
+ - /fs_hsdr_like/FS_HsdR_like_HP.cif
---
::
@@ -55,7 +55,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /fs_hsdr_like/FS_HsdR_like_HdrR.pdb
+ - /fs_hsdr_like/FS_HsdR_like_HdrR.cif
---
::
diff --git a/content/3.defense-systems/fs_sma.md b/content/3.defense-systems/fs_sma.md
index 31120a93..d9cce065 100644
--- a/content/3.defense-systems/fs_sma.md
+++ b/content/3.defense-systems/fs_sma.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the FS_Sma system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /fs_sma/FS_Sma__Sma.pdb
+ - /fs_sma/FS_Sma__Sma.cif
---
::
diff --git a/content/3.defense-systems/gabija.md b/content/3.defense-systems/gabija.md
index d255ba39..04a0a6c8 100644
--- a/content/3.defense-systems/gabija.md
+++ b/content/3.defense-systems/gabija.md
@@ -63,8 +63,8 @@ Proportion of genome encoding the Gabija system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gabija/Gabija.Gabija__GajA.0.V.pdb
- - /gabija/Gabija.Gabija_GajB.0.V.pdb
+ - /gabija/Gabija.Gabija__GajA.0.V.cif
+ - /gabija/Gabija.Gabija_GajB.0.V.cif
---
::
diff --git a/content/3.defense-systems/gao_ape.md b/content/3.defense-systems/gao_ape.md
index a5da96e7..1cc62074 100644
--- a/content/3.defense-systems/gao_ape.md
+++ b/content/3.defense-systems/gao_ape.md
@@ -56,7 +56,7 @@ Proportion of genome encoding the Gao_Ape system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gao_ape/Gao_Ape__ApeA.pdb
+ - /gao_ape/Gao_Ape__ApeA.cif
---
::
diff --git a/content/3.defense-systems/gao_her.md b/content/3.defense-systems/gao_her.md
index 1f5cf399..665de18d 100644
--- a/content/3.defense-systems/gao_her.md
+++ b/content/3.defense-systems/gao_her.md
@@ -49,8 +49,8 @@ Proportion of genome encoding the Gao_Her system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gao_her/Gao_Her_DUF.Gao_Her_DUF__DUF4297.0.V.pdb
- - /gao_her/Gao_Her_DUF.Gao_Her_DUF__HerA_DUF.0.V.pdb
+ - /gao_her/Gao_Her_DUF.Gao_Her_DUF__DUF4297.0.V.cif
+ - /gao_her/Gao_Her_DUF.Gao_Her_DUF__HerA_DUF.0.V.cif
---
::
@@ -61,8 +61,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /gao_her/Gao_Her_SIR.Gao_Her_SIR__HerA_SIR2.0.V.pdb
- - /gao_her/Gao_Her_SIR.Gao_Her_SIR__SIR2.0.V.pdb
+ - /gao_her/Gao_Her_SIR.Gao_Her_SIR__HerA_SIR2.0.V.cif
+ - /gao_her/Gao_Her_SIR.Gao_Her_SIR__SIR2.0.V.cif
---
::
diff --git a/content/3.defense-systems/gao_hhe.md b/content/3.defense-systems/gao_hhe.md
index 9d6f96e5..5b20fd74 100644
--- a/content/3.defense-systems/gao_hhe.md
+++ b/content/3.defense-systems/gao_hhe.md
@@ -54,7 +54,7 @@ Proportion of genome encoding the Gao_Hhe system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gao_hhe/Gao_Hhe__HheA.pdb
+ - /gao_hhe/Gao_Hhe__HheA.cif
---
::
diff --git a/content/3.defense-systems/gao_iet.md b/content/3.defense-systems/gao_iet.md
index a2485e4d..65c30c59 100644
--- a/content/3.defense-systems/gao_iet.md
+++ b/content/3.defense-systems/gao_iet.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the Gao_Iet system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gao_iet/Gao_Iet.Gao_Iet__IetA.0.V.pdb
- - /gao_iet/Gao_Iet.Gao_Iet__IetS.0.V.pdb
+ - /gao_iet/Gao_Iet.Gao_Iet__IetA.0.V.cif
+ - /gao_iet/Gao_Iet.Gao_Iet__IetS.0.V.cif
---
::
diff --git a/content/3.defense-systems/gao_mza.md b/content/3.defense-systems/gao_mza.md
index 73877416..ff01df63 100644
--- a/content/3.defense-systems/gao_mza.md
+++ b/content/3.defense-systems/gao_mza.md
@@ -54,11 +54,11 @@ Proportion of genome encoding the Gao_Mza system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gao_mza/Gao_Mza.Gao_Mza__MzaE.0.V.pdb
- - /gao_mza/Gao_Mza.Gao_Mza__MzaD.0.V.pdb
- - /gao_mza/Gao_Mza.Gao_Mza__MzaC.0.V.pdb
- - /gao_mza/Gao_Mza.Gao_Mza__MzaB.0.V.pdb
- - /gao_mza/Gao_Mza.Gao_Mza__MzaA.0.V.pdb
+ - /gao_mza/Gao_Mza.Gao_Mza__MzaE.0.V.cif
+ - /gao_mza/Gao_Mza.Gao_Mza__MzaD.0.V.cif
+ - /gao_mza/Gao_Mza.Gao_Mza__MzaC.0.V.cif
+ - /gao_mza/Gao_Mza.Gao_Mza__MzaB.0.V.cif
+ - /gao_mza/Gao_Mza.Gao_Mza__MzaA.0.V.cif
---
::
diff --git a/content/3.defense-systems/gao_ppl.md b/content/3.defense-systems/gao_ppl.md
index f88fe77c..0be59fdb 100644
--- a/content/3.defense-systems/gao_ppl.md
+++ b/content/3.defense-systems/gao_ppl.md
@@ -44,7 +44,7 @@ Proportion of genome encoding the Gao_Ppl system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gao_ppl/Gao_Ppl__PplA.pdb
+ - /gao_ppl/Gao_Ppl__PplA.cif
---
::
diff --git a/content/3.defense-systems/gao_qat.md b/content/3.defense-systems/gao_qat.md
index ecdaaaf4..6480be67 100644
--- a/content/3.defense-systems/gao_qat.md
+++ b/content/3.defense-systems/gao_qat.md
@@ -45,10 +45,10 @@ Proportion of genome encoding the Gao_Qat system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gao_qat/Gao_Qat.Gao_Qat__QatA.0.V.pdb
- - /gao_qat/Gao_Qat.Gao_Qat__QatB.0.V.pdb
- - /gao_qat/Gao_Qat.Gao_Qat__QatC.0.V.pdb
- - /gao_qat/Gao_Qat.Gao_Qat__QatD.0.V.pdb
+ - /gao_qat/Gao_Qat.Gao_Qat__QatA.0.V.cif
+ - /gao_qat/Gao_Qat.Gao_Qat__QatB.0.V.cif
+ - /gao_qat/Gao_Qat.Gao_Qat__QatC.0.V.cif
+ - /gao_qat/Gao_Qat.Gao_Qat__QatD.0.V.cif
---
::
diff --git a/content/3.defense-systems/gao_rl.md b/content/3.defense-systems/gao_rl.md
index 5f77504e..48e9a4a1 100644
--- a/content/3.defense-systems/gao_rl.md
+++ b/content/3.defense-systems/gao_rl.md
@@ -56,10 +56,10 @@ Proportion of genome encoding the Gao_RL system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gao_rl/Gao_RL.Gao_RL__RL_A.0.V.pdb
- - /gao_rl/Gao_RL.Gao_RL__RL_D.0.V.pdb
- - /gao_rl/Gao_RL.Gao_RL__RL_B.0.V.pdb
- - /gao_rl/Gao_RL.Gao_RL__RL_C.0.V.pdb
+ - /gao_rl/Gao_RL.Gao_RL__RL_A.0.V.cif
+ - /gao_rl/Gao_RL.Gao_RL__RL_D.0.V.cif
+ - /gao_rl/Gao_RL.Gao_RL__RL_B.0.V.cif
+ - /gao_rl/Gao_RL.Gao_RL__RL_C.0.V.cif
---
::
diff --git a/content/3.defense-systems/gao_tery.md b/content/3.defense-systems/gao_tery.md
index d6278bb7..f9f854a4 100644
--- a/content/3.defense-systems/gao_tery.md
+++ b/content/3.defense-systems/gao_tery.md
@@ -44,9 +44,9 @@ Proportion of genome encoding the Gao_TerY system for the 14 phyla with more tha
---
height: 700
dataUrls:
- - /gao_tery/Gao_TerY.Gao_TerY__TerYA.0.V.pdb
- - /gao_tery/Gao_TerY.Gao_TerY__TerYB.0.V.pdb
- - /gao_tery/Gao_TerY.Gao_TerY__TerYC.0.V.pdb
+ - /gao_tery/Gao_TerY.Gao_TerY__TerYA.0.V.cif
+ - /gao_tery/Gao_TerY.Gao_TerY__TerYB.0.V.cif
+ - /gao_tery/Gao_TerY.Gao_TerY__TerYC.0.V.cif
---
::
diff --git a/content/3.defense-systems/gao_tmn.md b/content/3.defense-systems/gao_tmn.md
index d4cc024c..20937475 100644
--- a/content/3.defense-systems/gao_tmn.md
+++ b/content/3.defense-systems/gao_tmn.md
@@ -55,7 +55,7 @@ Proportion of genome encoding the Gao_Tmn system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gao_tmn/Gao_Tmn__TmnA.pdb
+ - /gao_tmn/Gao_Tmn__TmnA.cif
---
::
diff --git a/content/3.defense-systems/gao_upx.md b/content/3.defense-systems/gao_upx.md
index f83ae2c2..3ea6b9d5 100644
--- a/content/3.defense-systems/gao_upx.md
+++ b/content/3.defense-systems/gao_upx.md
@@ -50,7 +50,7 @@ Proportion of genome encoding the Gao_Upx system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /gao_upx/Gao_Upx__UpxA.pdb
+ - /gao_upx/Gao_Upx__UpxA.cif
---
::
diff --git a/content/3.defense-systems/gaps1.md b/content/3.defense-systems/gaps1.md
index 14b2de50..476d7eee 100644
--- a/content/3.defense-systems/gaps1.md
+++ b/content/3.defense-systems/gaps1.md
@@ -54,7 +54,7 @@ Proportion of genome encoding the GAPS1 system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /gaps1/GAPS1__GAPS1.pdb
+ - /gaps1/GAPS1__GAPS1.cif
---
::
diff --git a/content/3.defense-systems/gaps2.md b/content/3.defense-systems/gaps2.md
index 528a69af..0ac62e66 100644
--- a/content/3.defense-systems/gaps2.md
+++ b/content/3.defense-systems/gaps2.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the GAPS2 system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /gaps2/GAPS2__GAPS2.pdb
+ - /gaps2/GAPS2__GAPS2.cif
---
::
diff --git a/content/3.defense-systems/gaps4.md b/content/3.defense-systems/gaps4.md
index f1d8c806..cf34d5b5 100644
--- a/content/3.defense-systems/gaps4.md
+++ b/content/3.defense-systems/gaps4.md
@@ -44,8 +44,8 @@ Proportion of genome encoding the GAPS4 system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /gaps4/GAPS4__GAPS4a.pdb
- - /gaps4/GAPS4__GAPS4b.pdb
+ - /gaps4/GAPS4__GAPS4a.cif
+ - /gaps4/GAPS4__GAPS4b.cif
---
::
diff --git a/content/3.defense-systems/gaps6.md b/content/3.defense-systems/gaps6.md
index f2258460..74be54db 100644
--- a/content/3.defense-systems/gaps6.md
+++ b/content/3.defense-systems/gaps6.md
@@ -44,8 +44,8 @@ Proportion of genome encoding the GAPS6 system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /gaps6/GAPS6__GAPS6a.pdb
- - /gaps6/GAPS6__GAPS6b.pdb
+ - /gaps6/GAPS6__GAPS6a.cif
+ - /gaps6/GAPS6__GAPS6b.cif
---
::
diff --git a/content/3.defense-systems/gasdermin.md b/content/3.defense-systems/gasdermin.md
index 792766c7..194afdb1 100644
--- a/content/3.defense-systems/gasdermin.md
+++ b/content/3.defense-systems/gasdermin.md
@@ -57,12 +57,12 @@ Proportion of genome encoding the GasderMIN system for the 14 phyla with more th
---
height: 700
dataUrls:
- - /gasdermin/GasderMIN__bGSDM.pdb
- - /gasdermin/GasderMIN__Protease1.pdb
- - /gasdermin/GasderMIN__Protease2.pdb
- - /gasdermin/GasderMIN__ATPase.pdb
- - /gasdermin/GasderMIN__Protease.pdb
- - /gasdermin/GasderMIN__bGSDM1.pdb
+ - /gasdermin/GasderMIN__bGSDM.cif
+ - /gasdermin/GasderMIN__Protease1.cif
+ - /gasdermin/GasderMIN__Protease2.cif
+ - /gasdermin/GasderMIN__ATPase.cif
+ - /gasdermin/GasderMIN__Protease.cif
+ - /gasdermin/GasderMIN__bGSDM1.cif
---
::
diff --git a/content/3.defense-systems/hachiman.md b/content/3.defense-systems/hachiman.md
index f2b53acd..1da92818 100644
--- a/content/3.defense-systems/hachiman.md
+++ b/content/3.defense-systems/hachiman.md
@@ -51,8 +51,8 @@ Proportion of genome encoding the Hachiman system for the 14 phyla with more tha
---
height: 700
dataUrls:
- - /hachiman/Hachiman.Hachiman__HamB.0.V.pdb
- - /hachiman/Hachiman.Hachiman__HamA.0.V.pdb
+ - /hachiman/Hachiman.Hachiman__HamB.0.V.cif
+ - /hachiman/Hachiman.Hachiman__HamA.0.V.cif
---
::
diff --git a/content/3.defense-systems/hna.md b/content/3.defense-systems/hna.md
index 5134b844..d87ab663 100644
--- a/content/3.defense-systems/hna.md
+++ b/content/3.defense-systems/hna.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the Hna system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /hna/Hna__Hna.pdb
+ - /hna/Hna__Hna.cif
---
::
diff --git a/content/3.defense-systems/isg15-like.md b/content/3.defense-systems/isg15-like.md
index 242a75ed..2e6fb72c 100644
--- a/content/3.defense-systems/isg15-like.md
+++ b/content/3.defense-systems/isg15-like.md
@@ -45,10 +45,10 @@ Proportion of genome encoding the ISG15-like system for the 14 phyla with more t
---
height: 700
dataUrls:
- - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
---
::
@@ -58,10 +58,10 @@ dataUrls:
---
height: 700
dataUrls:
- - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
---
::
@@ -71,10 +71,10 @@ dataUrls:
---
height: 700
dataUrls:
- - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
---
::
@@ -84,10 +84,10 @@ dataUrls:
---
height: 700
dataUrls:
- - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
---
::
@@ -97,10 +97,10 @@ dataUrls:
---
height: 700
dataUrls:
- - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.pdb
- - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.pdb
+ - /isg15-like/ISG15-like.ISG15-like__BilA.2.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilB.4.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilC.2.V.cif
+ - /isg15-like/ISG15-like.ISG15-like__BilD.3.V.cif
---
::
diff --git a/content/3.defense-systems/jukab.md b/content/3.defense-systems/jukab.md
index c153378b..61f8bb4e 100644
--- a/content/3.defense-systems/jukab.md
+++ b/content/3.defense-systems/jukab.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the JukAB system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /jukab/JukAB__JukB.pdb
- - /jukab/JukAB__JukA.pdb
+ - /jukab/JukAB__JukB.cif
+ - /jukab/JukAB__JukA.cif
---
::
diff --git a/content/3.defense-systems/kiwa.md b/content/3.defense-systems/kiwa.md
index 87a2bc70..0c5ddce4 100644
--- a/content/3.defense-systems/kiwa.md
+++ b/content/3.defense-systems/kiwa.md
@@ -56,8 +56,8 @@ Proportion of genome encoding the Kiwa system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /kiwa/Kiwa.Kiwa__KwaB.0.V.pdb
- - /kiwa/Kiwa.Kiwa__KwaA.0.V.pdb
+ - /kiwa/Kiwa.Kiwa__KwaB.0.V.cif
+ - /kiwa/Kiwa.Kiwa__KwaA.0.V.cif
---
::
diff --git a/content/3.defense-systems/lamassu-fam.md b/content/3.defense-systems/lamassu-fam.md
index 8b5be319..a7dfbe54 100644
--- a/content/3.defense-systems/lamassu-fam.md
+++ b/content/3.defense-systems/lamassu-fam.md
@@ -105,8 +105,8 @@ Proportion of genome encoding the Lamassu-Fam system for the 14 phyla with more
---
height: 700
dataUrls:
- - /lamassu-fam/Lamassu-Amidase.Lamassu-Fam__LmuA_effector_Amidase.0.DF.pdb
- - /lamassu-fam/Lamassu-Amidase.Lamassu-Fam__LmuB_SMC_Amidase.0.DF.pdb
+ - /lamassu-fam/Lamassu-Amidase.Lamassu-Fam__LmuA_effector_Amidase.0.DF.cif
+ - /lamassu-fam/Lamassu-Amidase.Lamassu-Fam__LmuB_SMC_Amidase.0.DF.cif
---
::
@@ -117,9 +117,9 @@ dataUrls:
---
height: 700
dataUrls:
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuA_effector_Cap4_nuclease_II.0.DF.pdb
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuC_acc_Cap4_nuclease.0.DF.pdb
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II.0.DF.pdb
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuA_effector_Cap4_nuclease_II.0.DF.cif
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuC_acc_Cap4_nuclease.0.DF.cif
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuB_SMC_Cap4_nuclease_II.0.DF.cif
---
::
@@ -129,9 +129,9 @@ dataUrls:
---
height: 700
dataUrls:
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuA_effector_Cap4_nuclease.1.DF.pdb
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam_undetected_LmuC.1.DF.pdb
- - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuB_SMC_Cap4_nuclease.1.DF.pdb
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuA_effector_Cap4_nuclease.1.DF.cif
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam_undetected_LmuC.1.DF.cif
+ - /lamassu-fam/Lamassu-Cap4_nuclease.Lamassu-Fam__LmuB_SMC_Cap4_nuclease.1.DF.cif
---
::
@@ -142,9 +142,9 @@ dataUrls:
---
height: 700
dataUrls:
- - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuB_SMC_FMO.0.DF.pdb
- - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuC_acc_FMO.0.DF.pdb
- - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuA_effector_FMO.0.DF.pdb
+ - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuB_SMC_FMO.0.DF.cif
+ - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuC_acc_FMO.0.DF.cif
+ - /lamassu-fam/Lamassu-FMO.Lamassu-Fam__LmuA_effector_FMO.0.DF.cif
---
::
@@ -155,10 +155,10 @@ dataUrls:
---
height: 700
dataUrls:
- - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuA_effector_Hydrolase.0.V.pdb
- - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuA_effector_Protease.0.V.pdb
- - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuC_acc_hydrolase_protease.0.V.pdb
- - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuB_SMC_Hydrolase_protease.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuA_effector_Hydrolase.0.V.cif
+ - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuA_effector_Protease.0.V.cif
+ - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuC_acc_hydrolase_protease.0.V.cif
+ - /lamassu-fam/Lamassu-Fam_Hydrolase_Protease.Lamassu-Fam__LmuB_SMC_Hydrolase_protease.0.V.cif
---
::
@@ -169,9 +169,9 @@ dataUrls:
---
height: 700
dataUrls:
- - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuA_effector_Mrr.0.V.pdb
- - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuC_acc_Mrr.0.V.pdb
- - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuB_SMC_Mrr.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuA_effector_Mrr.0.V.cif
+ - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuC_acc_Mrr.0.V.cif
+ - /lamassu-fam/Lamassu-Fam_Mrr.Lamassu-Fam__LmuB_SMC_Mrr.0.V.cif
---
::
@@ -182,12 +182,12 @@ dataUrls:
---
height: 700
dataUrls:
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuA_effector_PDDEXK.0.V.pdb
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuB_SMC_PDDEXK.0.V.pdb
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuC_acc_PDDEXK.0.V.pdb
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuC_acc_PDDEXK.0.V.pdb
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuB_SMC_PDDEXK.0.V.pdb
- - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuA_effector_PDDEXK.0.V.pdb
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuA_effector_PDDEXK.0.V.cif
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuB_SMC_PDDEXK.0.V.cif
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuC_acc_PDDEXK.0.V.cif
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuC_acc_PDDEXK.0.V.cif
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuB_SMC_PDDEXK.0.V.cif
+ - /lamassu-fam/Lamassu-Fam_PDDEXK.Lamassu-Fam__LmuA_effector_PDDEXK.0.V.cif
---
::
@@ -198,9 +198,9 @@ dataUrls:
---
height: 700
dataUrls:
- - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuB_SMC_hypothetical.0.DF.pdb
- - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuC_acc_hypothetical.0.DF.pdb
- - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuA_effector_hypothetical.0.DF.pdb
+ - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuB_SMC_hypothetical.0.DF.cif
+ - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuC_acc_hypothetical.0.DF.cif
+ - /lamassu-fam/Lamassu-Hypothetical.Lamassu-Fam__LmuA_effector_hypothetical.0.DF.cif
---
::
@@ -211,9 +211,9 @@ dataUrls:
---
height: 700
dataUrls:
- - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuB_SMC_Lipase.0.DF.pdb
- - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuC_acc_Lipase.0.DF.pdb
- - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuA_effector_Lipase.0.DF.pdb
+ - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuB_SMC_Lipase.0.DF.cif
+ - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuC_acc_Lipase.0.DF.cif
+ - /lamassu-fam/Lamassu-Lipase.Lamassu-Fam__LmuA_effector_Lipase.0.DF.cif
---
::
@@ -224,9 +224,9 @@ dataUrls:
---
height: 700
dataUrls:
- - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuB_SMC_Sir2.0.DF.pdb
- - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuC_acc_Sir2.0.DF.pdb
- - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuA_effector_Sir2.0.DF.pdb
+ - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuB_SMC_Sir2.0.DF.cif
+ - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuC_acc_Sir2.0.DF.cif
+ - /lamassu-fam/Lamassu-Sir2.Lamassu-Fam__LmuA_effector_Sir2.0.DF.cif
---
::
diff --git a/content/3.defense-systems/lit.md b/content/3.defense-systems/lit.md
index 55de9768..cf1d9bdb 100644
--- a/content/3.defense-systems/lit.md
+++ b/content/3.defense-systems/lit.md
@@ -60,7 +60,7 @@ Proportion of genome encoding the Lit system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /lit/Lit__Lit.pdb
+ - /lit/Lit__Lit.cif
---
::
diff --git a/content/3.defense-systems/mads.md b/content/3.defense-systems/mads.md
index 4c44664d..59eac5c4 100644
--- a/content/3.defense-systems/mads.md
+++ b/content/3.defense-systems/mads.md
@@ -45,13 +45,13 @@ Proportion of genome encoding the MADS system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /mads/MADS__mad8.pdb
- - /mads/MADS__mad7.pdb
- - /mads/MADS__mad4.pdb
- - /mads/MADS__mad3.pdb
- - /mads/MADS__mad1.pdb
- - /mads/MADS__mad5.pdb
- - /mads/MADS__mad2.pdb
+ - /mads/MADS__mad8.cif
+ - /mads/MADS__mad7.cif
+ - /mads/MADS__mad4.cif
+ - /mads/MADS__mad3.cif
+ - /mads/MADS__mad1.cif
+ - /mads/MADS__mad5.cif
+ - /mads/MADS__mad2.cif
---
::
diff --git a/content/3.defense-systems/menshen.md b/content/3.defense-systems/menshen.md
index 6678c81f..aae29f8c 100644
--- a/content/3.defense-systems/menshen.md
+++ b/content/3.defense-systems/menshen.md
@@ -56,9 +56,9 @@ Proportion of genome encoding the Menshen system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /menshen/Menshen.Menshen__NsnA.0.V.pdb
- - /menshen/Menshen.Menshen__NsnB.0.V.pdb
- - /menshen/Menshen.Menshen__NsnC.0.V.pdb
+ - /menshen/Menshen.Menshen__NsnA.0.V.cif
+ - /menshen/Menshen.Menshen__NsnB.0.V.cif
+ - /menshen/Menshen.Menshen__NsnC.0.V.cif
---
::
diff --git a/content/3.defense-systems/mmb_gp29_gp30.md b/content/3.defense-systems/mmb_gp29_gp30.md
index 1985314e..7b214492 100644
--- a/content/3.defense-systems/mmb_gp29_gp30.md
+++ b/content/3.defense-systems/mmb_gp29_gp30.md
@@ -50,8 +50,8 @@ Proportion of genome encoding the MMB_gp29_gp30 system for the 14 phyla with mor
---
height: 700
dataUrls:
- - /mmb_gp29_gp30/MMB_gp29_gp30__gp29.pdb
- - /mmb_gp29_gp30/MMB_gp29_gp30__gp30.pdb
+ - /mmb_gp29_gp30/MMB_gp29_gp30__gp29.cif
+ - /mmb_gp29_gp30/MMB_gp29_gp30__gp30.cif
---
::
diff --git a/content/3.defense-systems/mok_hok_sok.md b/content/3.defense-systems/mok_hok_sok.md
index ddcf152d..48ce106a 100644
--- a/content/3.defense-systems/mok_hok_sok.md
+++ b/content/3.defense-systems/mok_hok_sok.md
@@ -60,7 +60,7 @@ Proportion of genome encoding the Mok_Hok_Sok system for the 14 phyla with more
---
height: 700
dataUrls:
- - /mok_hok_sok/Mok_Hok_Sok__Hok.pdb
+ - /mok_hok_sok/Mok_Hok_Sok__Hok.cif
---
::
diff --git a/content/3.defense-systems/mokosh.md b/content/3.defense-systems/mokosh.md
index 0c365bcb..d52939e1 100644
--- a/content/3.defense-systems/mokosh.md
+++ b/content/3.defense-systems/mokosh.md
@@ -75,7 +75,7 @@ Proportion of genome encoding the Mokosh system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /mokosh/Mokosh_TypeI.Mokosh_TypeI__MkoB.0.V.pdb
+ - /mokosh/Mokosh_TypeI.Mokosh_TypeI__MkoB.0.V.cif
---
::
@@ -85,7 +85,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /mokosh/Mokosh_TypeI.Mokosh_TypeI__MkoB.0.V.pdb
+ - /mokosh/Mokosh_TypeI.Mokosh_TypeI__MkoB.0.V.cif
---
::
@@ -96,7 +96,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /mokosh/Mokosh_TypeII__MkoC.pdb
+ - /mokosh/Mokosh_TypeII__MkoC.cif
---
::
diff --git a/content/3.defense-systems/nhi.md b/content/3.defense-systems/nhi.md
index 08d379f4..c5c2b4c3 100644
--- a/content/3.defense-systems/nhi.md
+++ b/content/3.defense-systems/nhi.md
@@ -57,7 +57,7 @@ Proportion of genome encoding the Nhi system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /nhi/Nhi__Nhi.pdb
+ - /nhi/Nhi__Nhi.cif
---
::
diff --git a/content/3.defense-systems/nixi.md b/content/3.defense-systems/nixi.md
index ac4971e6..1e07155a 100644
--- a/content/3.defense-systems/nixi.md
+++ b/content/3.defense-systems/nixi.md
@@ -52,7 +52,7 @@ Proportion of genome encoding the NixI system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /nixi/NixI__NixI.pdb
+ - /nixi/NixI__NixI.cif
---
::
diff --git a/content/3.defense-systems/nlr.md b/content/3.defense-systems/nlr.md
index 9fb50ad8..f3188e13 100644
--- a/content/3.defense-systems/nlr.md
+++ b/content/3.defense-systems/nlr.md
@@ -49,7 +49,7 @@ Proportion of genome encoding the NLR system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /nlr/NLR_like_bNACHT01__NLR_like_bNACHT01.pdb
+ - /nlr/NLR_like_bNACHT01__NLR_like_bNACHT01.cif
---
::
@@ -60,7 +60,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /nlr/NLR_like_bNACHT09__NLR_like_bNACHT09.pdb
+ - /nlr/NLR_like_bNACHT09__NLR_like_bNACHT09.cif
---
::
diff --git a/content/3.defense-systems/old_exonuclease.md b/content/3.defense-systems/old_exonuclease.md
index 8359ab39..f1f4d4b7 100644
--- a/content/3.defense-systems/old_exonuclease.md
+++ b/content/3.defense-systems/old_exonuclease.md
@@ -55,7 +55,7 @@ Proportion of genome encoding the Old_exonuclease system for the 14 phyla with m
---
height: 700
dataUrls:
- - /old_exonuclease/Old_exonuclease__Old_exonuclease.pdb
+ - /old_exonuclease/Old_exonuclease__Old_exonuclease.cif
---
::
diff --git a/content/3.defense-systems/olokun.md b/content/3.defense-systems/olokun.md
index 4b48a329..9c1b1d68 100644
--- a/content/3.defense-systems/olokun.md
+++ b/content/3.defense-systems/olokun.md
@@ -61,8 +61,8 @@ Proportion of genome encoding the Olokun system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /olokun/Olokun.Olokun__OloA.0.V.pdb
- - /olokun/Olokun.Olokun__OloB.0.V.pdb
+ - /olokun/Olokun.Olokun__OloA.0.V.cif
+ - /olokun/Olokun.Olokun__OloB.0.V.cif
---
::
diff --git a/content/3.defense-systems/pago.md b/content/3.defense-systems/pago.md
index 86caf2b4..4a2e37c6 100644
--- a/content/3.defense-systems/pago.md
+++ b/content/3.defense-systems/pago.md
@@ -108,15 +108,15 @@ Proportion of genome encoding the pAgo system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /pago/pAgo__pAgo_LongA.pdb
- - /pago/pAgo__pAgo_LongB.pdb
- - /pago/pAgo__pAgo_S1A.pdb
- - /pago/pAgo__SIR2APAZ.pdb
- - /pago/pAgo__pAgo_S1B.pdb
- - /pago/pAgo__XAPAZ.pdb
- - /pago/pAgo__pAgo_S2B.pdb
- - /pago/pAgo__TIRAPAZ.pdb
- - /pago/pAgo__pAgo_SPARTA.pdb
+ - /pago/pAgo__pAgo_LongA.cif
+ - /pago/pAgo__pAgo_LongB.cif
+ - /pago/pAgo__pAgo_S1A.cif
+ - /pago/pAgo__SIR2APAZ.cif
+ - /pago/pAgo__pAgo_S1B.cif
+ - /pago/pAgo__XAPAZ.cif
+ - /pago/pAgo__pAgo_S2B.cif
+ - /pago/pAgo__TIRAPAZ.cif
+ - /pago/pAgo__pAgo_SPARTA.cif
---
::
diff --git a/content/3.defense-systems/panchino_gp28.md b/content/3.defense-systems/panchino_gp28.md
index b526b528..176bb544 100644
--- a/content/3.defense-systems/panchino_gp28.md
+++ b/content/3.defense-systems/panchino_gp28.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the Panchino_gp28 system for the 14 phyla with mor
---
height: 700
dataUrls:
- - /panchino_gp28/Panchino_gp28__gp28.pdb
+ - /panchino_gp28/Panchino_gp28__gp28.cif
---
::
diff --git a/content/3.defense-systems/paris.md b/content/3.defense-systems/paris.md
index 06b902d5..166b92ef 100644
--- a/content/3.defense-systems/paris.md
+++ b/content/3.defense-systems/paris.md
@@ -56,8 +56,8 @@ Proportion of genome encoding the Paris system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /paris/PARIS_I.PARIS_I__AAA_15.0.V.pdb
- - /paris/PARIS_I.Rst_PARIS__DUF4435.0.V.pdb
+ - /paris/PARIS_I.PARIS_I__AAA_15.0.V.cif
+ - /paris/PARIS_I.Rst_PARIS__DUF4435.0.V.cif
---
::
@@ -68,8 +68,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /paris/PARIS_I.Rst_PARIS__DUF4435.0.V.pdb
- - /paris/PARIS_II.PARIS_II__AAA_21.0.V.pdb
+ - /paris/PARIS_I.Rst_PARIS__DUF4435.0.V.cif
+ - /paris/PARIS_II.PARIS_II__AAA_21.0.V.cif
---
::
@@ -80,7 +80,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /paris/PARIS_II_merge__AAA_21_DUF4435.pdb
+ - /paris/PARIS_II_merge__AAA_21_DUF4435.cif
---
::
@@ -91,7 +91,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /paris/PARIS_I_merge__AAA_15_DUF4435.pdb
+ - /paris/PARIS_I_merge__AAA_15_DUF4435.cif
---
::
diff --git a/content/3.defense-systems/pd-lambda-1.md b/content/3.defense-systems/pd-lambda-1.md
index b09ecd28..2b6a6631 100644
--- a/content/3.defense-systems/pd-lambda-1.md
+++ b/content/3.defense-systems/pd-lambda-1.md
@@ -57,7 +57,7 @@ Proportion of genome encoding the PD-Lambda-1 system for the 14 phyla with more
---
height: 700
dataUrls:
- - /pd-lambda-1/PD-Lambda-1__PD-Lambda-1.pdb
+ - /pd-lambda-1/PD-Lambda-1__PD-Lambda-1.cif
---
::
diff --git a/content/3.defense-systems/pd-lambda-2.md b/content/3.defense-systems/pd-lambda-2.md
index e39dc537..60115406 100644
--- a/content/3.defense-systems/pd-lambda-2.md
+++ b/content/3.defense-systems/pd-lambda-2.md
@@ -45,9 +45,9 @@ Proportion of genome encoding the PD-Lambda-2 system for the 14 phyla with more
---
height: 700
dataUrls:
- - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_C.0.V.pdb
- - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_B.0.V.pdb
- - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_A.0.V.pdb
+ - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_C.0.V.cif
+ - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_B.0.V.cif
+ - /pd-lambda-2/PD-Lambda-2.PD-Lambda-2__PD-Lambda-2_A.0.V.cif
---
::
diff --git a/content/3.defense-systems/pd-lambda-3.md b/content/3.defense-systems/pd-lambda-3.md
index 06508b69..2ec3b7aa 100644
--- a/content/3.defense-systems/pd-lambda-3.md
+++ b/content/3.defense-systems/pd-lambda-3.md
@@ -54,9 +54,9 @@ Proportion of genome encoding the PD-Lambda-3 system for the 14 phyla with more
---
height: 700
dataUrls:
- - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_A.0.V.pdb
- - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_B.0.V.pdb
- - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_C.0.V.pdb
+ - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_A.0.V.cif
+ - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_B.0.V.cif
+ - /pd-lambda-3/PD-Lambda-3.PD-Lambda-3__PD-Lambda-3_C.0.V.cif
---
::
diff --git a/content/3.defense-systems/pd-lambda-4.md b/content/3.defense-systems/pd-lambda-4.md
index 7dc2f86c..cb1c78b4 100644
--- a/content/3.defense-systems/pd-lambda-4.md
+++ b/content/3.defense-systems/pd-lambda-4.md
@@ -44,8 +44,8 @@ Proportion of genome encoding the PD-Lambda-4 system for the 14 phyla with more
---
height: 700
dataUrls:
- - /pd-lambda-4/PD-Lambda-4.PD-Lambda-4__PD-Lambda-4_B.0.V.pdb
- - /pd-lambda-4/PD-Lambda-4.PD-Lambda-4__PD-Lambda-4_A.0.V.pdb
+ - /pd-lambda-4/PD-Lambda-4.PD-Lambda-4__PD-Lambda-4_B.0.V.cif
+ - /pd-lambda-4/PD-Lambda-4.PD-Lambda-4__PD-Lambda-4_A.0.V.cif
---
::
diff --git a/content/3.defense-systems/pd-lambda-5.md b/content/3.defense-systems/pd-lambda-5.md
index e19d460d..c76b61df 100644
--- a/content/3.defense-systems/pd-lambda-5.md
+++ b/content/3.defense-systems/pd-lambda-5.md
@@ -53,8 +53,8 @@ Proportion of genome encoding the PD-Lambda-5 system for the 14 phyla with more
---
height: 700
dataUrls:
- - /pd-lambda-5/PD-Lambda-5.PD-Lambda-5__PD-Lambda-5_A.0.V.pdb
- - /pd-lambda-5/PD-Lambda-5.PD-Lambda-5__PD-Lambda-5_B.0.V.pdb
+ - /pd-lambda-5/PD-Lambda-5.PD-Lambda-5__PD-Lambda-5_A.0.V.cif
+ - /pd-lambda-5/PD-Lambda-5.PD-Lambda-5__PD-Lambda-5_B.0.V.cif
---
::
diff --git a/content/3.defense-systems/pd-lambda-6.md b/content/3.defense-systems/pd-lambda-6.md
index 76136adc..990adbad 100644
--- a/content/3.defense-systems/pd-lambda-6.md
+++ b/content/3.defense-systems/pd-lambda-6.md
@@ -44,7 +44,7 @@ Proportion of genome encoding the PD-Lambda-6 system for the 14 phyla with more
---
height: 700
dataUrls:
- - /pd-lambda-6/PD-Lambda-6__PD-Lambda-6.pdb
+ - /pd-lambda-6/PD-Lambda-6__PD-Lambda-6.cif
---
::
diff --git a/content/3.defense-systems/pd-t4-1.md b/content/3.defense-systems/pd-t4-1.md
index 5b22a947..df7c7ef3 100644
--- a/content/3.defense-systems/pd-t4-1.md
+++ b/content/3.defense-systems/pd-t4-1.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the PD-T4-1 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t4-1/PD-T4-1__PD-T4-1.pdb
+ - /pd-t4-1/PD-T4-1__PD-T4-1.cif
---
::
diff --git a/content/3.defense-systems/pd-t4-10.md b/content/3.defense-systems/pd-t4-10.md
index 18d40210..98dce35f 100644
--- a/content/3.defense-systems/pd-t4-10.md
+++ b/content/3.defense-systems/pd-t4-10.md
@@ -54,8 +54,8 @@ Proportion of genome encoding the PD-T4-10 system for the 14 phyla with more tha
---
height: 700
dataUrls:
- - /pd-t4-10/PD-T4-10.PD-T4-10__PD-T4-10_B.0.V.pdb
- - /pd-t4-10/PD-T4-10.PD-T4-10__PD-T4-10_A.0.V.pdb
+ - /pd-t4-10/PD-T4-10.PD-T4-10__PD-T4-10_B.0.V.cif
+ - /pd-t4-10/PD-T4-10.PD-T4-10__PD-T4-10_A.0.V.cif
---
::
diff --git a/content/3.defense-systems/pd-t4-2.md b/content/3.defense-systems/pd-t4-2.md
index 1d2a11f3..2d853db9 100644
--- a/content/3.defense-systems/pd-t4-2.md
+++ b/content/3.defense-systems/pd-t4-2.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the PD-T4-2 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t4-2/PD-T4-2.PD-T4-2__PD-T4-2_A.0.DF.pdb
- - /pd-t4-2/PD-T4-2.PD-T4-2__PD-T4-2_B.0.DF.pdb
+ - /pd-t4-2/PD-T4-2.PD-T4-2__PD-T4-2_A.0.DF.cif
+ - /pd-t4-2/PD-T4-2.PD-T4-2__PD-T4-2_B.0.DF.cif
---
::
diff --git a/content/3.defense-systems/pd-t4-3.md b/content/3.defense-systems/pd-t4-3.md
index ea87f4c9..debef120 100644
--- a/content/3.defense-systems/pd-t4-3.md
+++ b/content/3.defense-systems/pd-t4-3.md
@@ -55,7 +55,7 @@ Proportion of genome encoding the PD-T4-3 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t4-3/PD-T4-3__PD-T4-3.pdb
+ - /pd-t4-3/PD-T4-3__PD-T4-3.cif
---
::
diff --git a/content/3.defense-systems/pd-t4-4.md b/content/3.defense-systems/pd-t4-4.md
index b7693c80..32b8b645 100644
--- a/content/3.defense-systems/pd-t4-4.md
+++ b/content/3.defense-systems/pd-t4-4.md
@@ -53,8 +53,8 @@ Proportion of genome encoding the PD-T4-4 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t4-4/PD-T4-4.PD-T4-4__PD-T4-4_B.0.V.pdb
- - /pd-t4-4/PD-T4-4.PD-T4-4__PD-T4-4_A.0.V.pdb
+ - /pd-t4-4/PD-T4-4.PD-T4-4__PD-T4-4_B.0.V.cif
+ - /pd-t4-4/PD-T4-4.PD-T4-4__PD-T4-4_A.0.V.cif
---
::
diff --git a/content/3.defense-systems/pd-t4-5.md b/content/3.defense-systems/pd-t4-5.md
index 37d1c023..6aecd831 100644
--- a/content/3.defense-systems/pd-t4-5.md
+++ b/content/3.defense-systems/pd-t4-5.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the PD-T4-5 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t4-5/PD-T4-5__PD-T4-5.pdb
+ - /pd-t4-5/PD-T4-5__PD-T4-5.cif
---
::
diff --git a/content/3.defense-systems/pd-t4-6.md b/content/3.defense-systems/pd-t4-6.md
index 6c419ca3..16599207 100644
--- a/content/3.defense-systems/pd-t4-6.md
+++ b/content/3.defense-systems/pd-t4-6.md
@@ -54,7 +54,7 @@ Proportion of genome encoding the PD-T4-6 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t4-6/PD-T4-6__PD-T4-6.pdb
+ - /pd-t4-6/PD-T4-6__PD-T4-6.cif
---
::
diff --git a/content/3.defense-systems/pd-t4-7.md b/content/3.defense-systems/pd-t4-7.md
index 0cb3aa71..8f82d3c2 100644
--- a/content/3.defense-systems/pd-t4-7.md
+++ b/content/3.defense-systems/pd-t4-7.md
@@ -56,7 +56,7 @@ Proportion of genome encoding the PD-T4-7 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t4-7/PD-T4-7__PD-T4-7.pdb
+ - /pd-t4-7/PD-T4-7__PD-T4-7.cif
---
::
diff --git a/content/3.defense-systems/pd-t4-8.md b/content/3.defense-systems/pd-t4-8.md
index dbc3b0c1..91807161 100644
--- a/content/3.defense-systems/pd-t4-8.md
+++ b/content/3.defense-systems/pd-t4-8.md
@@ -54,7 +54,7 @@ Proportion of genome encoding the PD-T4-8 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t4-8/PD-T4-8__PD-T4-8.pdb
+ - /pd-t4-8/PD-T4-8__PD-T4-8.cif
---
::
diff --git a/content/3.defense-systems/pd-t4-9.md b/content/3.defense-systems/pd-t4-9.md
index ee080a2e..b4236776 100644
--- a/content/3.defense-systems/pd-t4-9.md
+++ b/content/3.defense-systems/pd-t4-9.md
@@ -45,9 +45,9 @@ Proportion of genome encoding the PD-T4-9 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_A.0.V.pdb
- - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_B.0.V.pdb
- - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_C.0.V.pdb
+ - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_A.0.V.cif
+ - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_B.0.V.cif
+ - /pd-t4-9/PD-T4-9.PD-T4-9__PD-T4-9_C.0.V.cif
---
::
diff --git a/content/3.defense-systems/pd-t7-1.md b/content/3.defense-systems/pd-t7-1.md
index 2ea58ee0..777fd7b6 100644
--- a/content/3.defense-systems/pd-t7-1.md
+++ b/content/3.defense-systems/pd-t7-1.md
@@ -44,7 +44,7 @@ Proportion of genome encoding the PD-T7-1 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t7-1/PD-T7-1__PD-T7-1.pdb
+ - /pd-t7-1/PD-T7-1__PD-T7-1.cif
---
::
diff --git a/content/3.defense-systems/pd-t7-2.md b/content/3.defense-systems/pd-t7-2.md
index 39a84ff6..dff84b32 100644
--- a/content/3.defense-systems/pd-t7-2.md
+++ b/content/3.defense-systems/pd-t7-2.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the PD-T7-2 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t7-2/PD-T7-2.PD-T7-2__PD-T7-2_B.0.V.pdb
- - /pd-t7-2/PD-T7-2.PD-T7-2__PD-T7-2_A.0.V.pdb
+ - /pd-t7-2/PD-T7-2.PD-T7-2__PD-T7-2_B.0.V.cif
+ - /pd-t7-2/PD-T7-2.PD-T7-2__PD-T7-2_A.0.V.cif
---
::
diff --git a/content/3.defense-systems/pd-t7-3.md b/content/3.defense-systems/pd-t7-3.md
index 7ff45688..07118a77 100644
--- a/content/3.defense-systems/pd-t7-3.md
+++ b/content/3.defense-systems/pd-t7-3.md
@@ -54,7 +54,7 @@ Proportion of genome encoding the PD-T7-3 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t7-3/PD-T7-3__PD-T7-3.pdb
+ - /pd-t7-3/PD-T7-3__PD-T7-3.cif
---
::
diff --git a/content/3.defense-systems/pd-t7-4.md b/content/3.defense-systems/pd-t7-4.md
index 3d1085e1..6b80d4a5 100644
--- a/content/3.defense-systems/pd-t7-4.md
+++ b/content/3.defense-systems/pd-t7-4.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the PD-T7-4 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t7-4/PD-T7-4__PD-T7-4.pdb
+ - /pd-t7-4/PD-T7-4__PD-T7-4.cif
---
::
diff --git a/content/3.defense-systems/pd-t7-5.md b/content/3.defense-systems/pd-t7-5.md
index 34db3bbb..1b97e8c5 100644
--- a/content/3.defense-systems/pd-t7-5.md
+++ b/content/3.defense-systems/pd-t7-5.md
@@ -44,7 +44,7 @@ Proportion of genome encoding the PD-T7-5 system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pd-t7-5/PD-T7-5__PD-T7-5.pdb
+ - /pd-t7-5/PD-T7-5__PD-T7-5.cif
---
::
diff --git a/content/3.defense-systems/pfiat.md b/content/3.defense-systems/pfiat.md
index ebfbe341..4f3afebf 100644
--- a/content/3.defense-systems/pfiat.md
+++ b/content/3.defense-systems/pfiat.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the PfiAT system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /pfiat/PfiAT.PfiAT__PfiA.0.V.pdb
- - /pfiat/PfiAT.PfiAT__PfiT.0.V.pdb
+ - /pfiat/PfiAT.PfiAT__PfiA.0.V.cif
+ - /pfiat/PfiAT.PfiAT__PfiT.0.V.cif
---
::
diff --git a/content/3.defense-systems/pif.md b/content/3.defense-systems/pif.md
index 0785faf0..83bd65b9 100644
--- a/content/3.defense-systems/pif.md
+++ b/content/3.defense-systems/pif.md
@@ -59,8 +59,8 @@ Proportion of genome encoding the Pif system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /pif/Pif.Pif__PifA.0.V.pdb
- - /pif/Pif.Pif__PifC.0.V.pdb
+ - /pif/Pif.Pif__PifA.0.V.cif
+ - /pif/Pif.Pif__PifC.0.V.cif
---
::
diff --git a/content/3.defense-systems/prrc.md b/content/3.defense-systems/prrc.md
index 8e7517d5..04018925 100644
--- a/content/3.defense-systems/prrc.md
+++ b/content/3.defense-systems/prrc.md
@@ -59,8 +59,8 @@ Proportion of genome encoding the PrrC system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /prrc/PrrC__EcoprrI.pdb
- - /prrc/PrrC__PrrC.pdb
+ - /prrc/PrrC__EcoprrI.cif
+ - /prrc/PrrC__PrrC.cif
---
::
@@ -71,8 +71,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /prrc/RM__Type_I_S.pdb
- - /prrc/RM__Type_I_REases.pdb
+ - /prrc/RM__Type_I_S.cif
+ - /prrc/RM__Type_I_REases.cif
---
::
diff --git a/content/3.defense-systems/psyrta.md b/content/3.defense-systems/psyrta.md
index 6e1d4fa9..d6752dd0 100644
--- a/content/3.defense-systems/psyrta.md
+++ b/content/3.defense-systems/psyrta.md
@@ -75,8 +75,8 @@ Proportion of genome encoding the PsyrTA system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /psyrta/PsyrTA.PsyrTA__PsyrT.0.V.pdb
- - /psyrta/PsyrTA.PsyrTA__PsyrA.0.V.pdb
+ - /psyrta/PsyrTA.PsyrTA__PsyrT.0.V.cif
+ - /psyrta/PsyrTA.PsyrTA__PsyrA.0.V.cif
---
::
diff --git a/content/3.defense-systems/pycsar.md b/content/3.defense-systems/pycsar.md
index 6a6469e0..77c07d53 100644
--- a/content/3.defense-systems/pycsar.md
+++ b/content/3.defense-systems/pycsar.md
@@ -47,8 +47,8 @@ Proportion of genome encoding the Pycsar system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /pycsar/Pycsar.Pycsar__AG_cyclase.1.V.pdb
- - /pycsar/Pycsar.CBASS__TIR.0.V.pdb
+ - /pycsar/Pycsar.Pycsar__AG_cyclase.1.V.cif
+ - /pycsar/Pycsar.CBASS__TIR.0.V.cif
---
::
@@ -58,8 +58,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /pycsar/Pycsar.CBASS_TM.1.V.pdb
- - /pycsar/Pycsar.Pycsar__AG_cyclase.1.V.pdb
+ - /pycsar/Pycsar.CBASS_TM.1.V.cif
+ - /pycsar/Pycsar.Pycsar__AG_cyclase.1.V.cif
---
::
diff --git a/content/3.defense-systems/radar.md b/content/3.defense-systems/radar.md
index 0510cece..fe2b0087 100644
--- a/content/3.defense-systems/radar.md
+++ b/content/3.defense-systems/radar.md
@@ -103,8 +103,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /radar/radar_I.radar_I__rdrB_I.0.V.pdb
- - /radar/radar_I.radar_I__rdrA_I.0.V.pdb
+ - /radar/radar_I.radar_I__rdrB_I.0.V.cif
+ - /radar/radar_I.radar_I__rdrA_I.0.V.cif
---
::
@@ -115,9 +115,9 @@ dataUrls:
---
height: 700
dataUrls:
- - /radar/radar_II.radar_II__rdrC_II.0.V.pdb
- - /radar/radar_II.radar_II__rdrB_II.0.V.pdb
- - /radar/radar_II.radar_II__rdrA_II.0.V.pdb
+ - /radar/radar_II.radar_II__rdrC_II.0.V.cif
+ - /radar/radar_II.radar_II__rdrB_II.0.V.cif
+ - /radar/radar_II.radar_II__rdrA_II.0.V.cif
---
::
diff --git a/content/3.defense-systems/retron.md b/content/3.defense-systems/retron.md
index a9daa09d..c70ac99b 100644
--- a/content/3.defense-systems/retron.md
+++ b/content/3.defense-systems/retron.md
@@ -132,7 +132,7 @@ Proportion of genome encoding the Retron system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /retron/RT_Ec67_SLATT.AbiA__AbiA_small_SLATT.Ec57.V.pdb
+ - /retron/RT_Ec67_SLATT.AbiA__AbiA_small_SLATT.Ec57.V.cif
---
::
@@ -142,7 +142,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/DRT_3.DRT_3__drt3a.0.V.pdb
+ - /retron/DRT_3.DRT_3__drt3a.0.V.cif
---
::
@@ -153,7 +153,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/Retron_II.Retron_II__NDT.Ec73.V.pdb
+ - /retron/Retron_II.Retron_II__NDT.Ec73.V.cif
---
::
@@ -163,7 +163,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/Retron_II.Retron_II__NDT.Ec73.V.pdb
+ - /retron/Retron_II.Retron_II__NDT.Ec73.V.cif
---
::
@@ -174,8 +174,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/Retron_III.Retron_III__PRTase.0.DF.pdb
- - /retron/Retron_III.Retron_III__WH.0.DF.pdb
+ - /retron/Retron_III.Retron_III__PRTase.0.DF.cif
+ - /retron/Retron_III.Retron_III__WH.0.DF.cif
---
::
@@ -185,7 +185,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/Retron_III.Retron_III__PRTase_WH.1.DF.pdb
+ - /retron/Retron_III.Retron_III__PRTase_WH.1.DF.cif
---
::
@@ -196,7 +196,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/Retron_IV.Retron_IV__2TM.Ec48.V.pdb
+ - /retron/Retron_IV.Retron_IV__2TM.Ec48.V.cif
---
::
@@ -207,8 +207,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/Retron_I_A.Retron__RT_Tot.Ec83.V.pdb
- - /retron/Retron_I_A.Retron_I_A__ATPase_TypeIA.Vc95.V.pdb
+ - /retron/Retron_I_A.Retron__RT_Tot.Ec83.V.cif
+ - /retron/Retron_I_A.Retron_I_A__ATPase_TypeIA.Vc95.V.cif
---
::
@@ -218,8 +218,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/Retron_I_A.Retron_I_A__ATPase_TypeIA.Vc95.V.pdb
- - /retron/Retron_I_A.Retron__RT_Tot.Ec83.V.pdb
+ - /retron/Retron_I_A.Retron_I_A__ATPase_TypeIA.Vc95.V.cif
+ - /retron/Retron_I_A.Retron__RT_Tot.Ec83.V.cif
---
::
@@ -230,7 +230,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/Retron_I_B.Retron_I_B__ATPase_TOPRIM_COG3593.Eco8.V.pdb
+ - /retron/Retron_I_B.Retron_I_B__ATPase_TOPRIM_COG3593.Eco8.V.cif
---
::
@@ -241,8 +241,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/Retron_VI.Retron_VI__HTH.0.DF.pdb
- - /retron/Retron_VI.Possible_Retron_VI__SP.0.DF.pdb
+ - /retron/Retron_VI.Retron_VI__HTH.0.DF.cif
+ - /retron/Retron_VI.Possible_Retron_VI__SP.0.DF.cif
---
::
@@ -253,7 +253,7 @@ dataUrls:
---
height: 700
dataUrls:
- - /retron/Retron_VII_2.Retron_VII_2__DUF3800.0.DF.pdb
+ - /retron/Retron_VII_2.Retron_VII_2__DUF3800.0.DF.cif
---
::
diff --git a/content/3.defense-systems/rexab.md b/content/3.defense-systems/rexab.md
index e02d4414..30f479b3 100644
--- a/content/3.defense-systems/rexab.md
+++ b/content/3.defense-systems/rexab.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the RexAB system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /rexab/RexAB.RexAB_RexB.0.V.pdb
- - /rexab/RexAB.RexAB_RexA.0.V.pdb
+ - /rexab/RexAB.RexAB_RexB.0.V.cif
+ - /rexab/RexAB.RexAB_RexA.0.V.cif
---
::
diff --git a/content/3.defense-systems/rloc.md b/content/3.defense-systems/rloc.md
index 273ede06..e8deba6f 100644
--- a/content/3.defense-systems/rloc.md
+++ b/content/3.defense-systems/rloc.md
@@ -46,7 +46,7 @@ Proportion of genome encoding the RloC system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /rloc/RloC__RloC.pdb
+ - /rloc/RloC__RloC.cif
---
::
diff --git a/content/3.defense-systems/rnlab.md b/content/3.defense-systems/rnlab.md
index 282a7875..6195477c 100644
--- a/content/3.defense-systems/rnlab.md
+++ b/content/3.defense-systems/rnlab.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the RnlAB system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /rnlab/RnlAB.RnlAB__RnlA.0.DF.pdb
- - /rnlab/RnlAB.RnlAB__RnlB.0.DF.pdb
+ - /rnlab/RnlAB.RnlAB__RnlA.0.DF.cif
+ - /rnlab/RnlAB.RnlAB__RnlB.0.DF.cif
---
::
diff --git a/content/3.defense-systems/rosmerta.md b/content/3.defense-systems/rosmerta.md
index 04f1ec00..db5e5087 100644
--- a/content/3.defense-systems/rosmerta.md
+++ b/content/3.defense-systems/rosmerta.md
@@ -56,8 +56,8 @@ Proportion of genome encoding the RosmerTA system for the 14 phyla with more tha
---
height: 700
dataUrls:
- - /rosmerta/RosmerTA.RosmerTA__RmrA.0.V.pdb
- - /rosmerta/RosmerTA.RosmerTA__RmrT.0.V.pdb
+ - /rosmerta/RosmerTA.RosmerTA__RmrA.0.V.cif
+ - /rosmerta/RosmerTA.RosmerTA__RmrT.0.V.cif
---
::
diff --git a/content/3.defense-systems/rst_2tm_1tm_tir.md b/content/3.defense-systems/rst_2tm_1tm_tir.md
index 8766ba22..0d680fdb 100644
--- a/content/3.defense-systems/rst_2tm_1tm_tir.md
+++ b/content/3.defense-systems/rst_2tm_1tm_tir.md
@@ -58,9 +58,9 @@ Proportion of genome encoding the Rst_2TM_1TM_TIR system for the 14 phyla with m
---
height: 700
dataUrls:
- - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_2TM_TIR.0.V.pdb
- - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_1TM_TIR.0.V.pdb
- - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_TIR_tm.0.V.pdb
+ - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_2TM_TIR.0.V.cif
+ - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_1TM_TIR.0.V.cif
+ - /rst_2tm_1tm_tir/Rst_2TM_1TM_TIR.Rst_2TM_1TM_TIR__Rst_TIR_tm.0.V.cif
## Experimental validation
diff --git a/content/3.defense-systems/rst_3hp.md b/content/3.defense-systems/rst_3hp.md
index 795e2eea..57095826 100644
--- a/content/3.defense-systems/rst_3hp.md
+++ b/content/3.defense-systems/rst_3hp.md
@@ -56,9 +56,9 @@ Proportion of genome encoding the Rst_3HP system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /rst_3hp/Rst_3HP.Rst_3HP__Hp1.0.V.pdb
- - /rst_3hp/Rst_3HP.Rst_3HP__Hp3.0.V.pdb
- - /rst_3hp/Rst_3HP.Rst_3HP__Hp2.0.V.pdb
+ - /rst_3hp/Rst_3HP.Rst_3HP__Hp1.0.V.cif
+ - /rst_3hp/Rst_3HP.Rst_3HP__Hp3.0.V.cif
+ - /rst_3hp/Rst_3HP.Rst_3HP__Hp2.0.V.cif
---
::
diff --git a/content/3.defense-systems/rst_duf4238.md b/content/3.defense-systems/rst_duf4238.md
index cda9b5f6..9a74d7ef 100644
--- a/content/3.defense-systems/rst_duf4238.md
+++ b/content/3.defense-systems/rst_duf4238.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the Rst_DUF4238 system for the 14 phyla with more
---
height: 700
dataUrls:
- - /rst_duf4238/Rst_DUF4238__DUF4238_Pers.pdb
+ - /rst_duf4238/Rst_DUF4238__DUF4238_Pers.cif
---
::
diff --git a/content/3.defense-systems/rst_gop_beta_cll.md b/content/3.defense-systems/rst_gop_beta_cll.md
index 6a49f423..1d287bb4 100644
--- a/content/3.defense-systems/rst_gop_beta_cll.md
+++ b/content/3.defense-systems/rst_gop_beta_cll.md
@@ -45,9 +45,9 @@ Proportion of genome encoding the Rst_gop_beta_cll system for the 14 phyla with
---
height: 700
dataUrls:
- - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__cll.0.V.pdb
- - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__gop.0.V.pdb
- - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__beta.0.V.pdb
+ - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__cll.0.V.cif
+ - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__gop.0.V.cif
+ - /rst_gop_beta_cll/Rst_gop_beta_cll.Rst_gop_beta_cll__beta.0.V.cif
---
::
diff --git a/content/3.defense-systems/rst_helicaseduf2290.md b/content/3.defense-systems/rst_helicaseduf2290.md
index 647094f8..448f5626 100644
--- a/content/3.defense-systems/rst_helicaseduf2290.md
+++ b/content/3.defense-systems/rst_helicaseduf2290.md
@@ -58,8 +58,8 @@ Proportion of genome encoding the Rst_HelicaseDUF2290 system for the 14 phyla wi
---
height: 700
dataUrls:
- - /rst_helicaseduf2290/Rst_HelicaseDUF2290.Rst_HelicaseDUF2290__DUF2290.0.V.pdb
- - /rst_helicaseduf2290/Rst_HelicaseDUF2290.Rst_HelicaseDUF2290__Helicase.0.V.pdb
+ - /rst_helicaseduf2290/Rst_HelicaseDUF2290.Rst_HelicaseDUF2290__DUF2290.0.V.cif
+ - /rst_helicaseduf2290/Rst_HelicaseDUF2290.Rst_HelicaseDUF2290__Helicase.0.V.cif
---
::
diff --git a/content/3.defense-systems/rst_hydrolase-3tm.md b/content/3.defense-systems/rst_hydrolase-3tm.md
index ecf86fe5..82bbc3fb 100644
--- a/content/3.defense-systems/rst_hydrolase-3tm.md
+++ b/content/3.defense-systems/rst_hydrolase-3tm.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the Rst_Hydrolase-3Tm system for the 14 phyla with
---
height: 700
dataUrls:
- - /rst_hydrolase-3tm/Rst_Hydrolase-Tm.Rst_Hydrolase-Tm__Hydrolase.0.V.pdb
- - /rst_hydrolase-3tm/Rst_Hydrolase-Tm.Rst_Hydrolase-Tm__Hydrolase-Tm.0.V.pdb
+ - /rst_hydrolase-3tm/Rst_Hydrolase-Tm.Rst_Hydrolase-Tm__Hydrolase.0.V.cif
+ - /rst_hydrolase-3tm/Rst_Hydrolase-Tm.Rst_Hydrolase-Tm__Hydrolase-Tm.0.V.cif
---
::
diff --git a/content/3.defense-systems/rst_rt-nitrilase-tm.md b/content/3.defense-systems/rst_rt-nitrilase-tm.md
index c1112119..8668f089 100644
--- a/content/3.defense-systems/rst_rt-nitrilase-tm.md
+++ b/content/3.defense-systems/rst_rt-nitrilase-tm.md
@@ -45,8 +45,8 @@ Proportion of genome encoding the Rst_RT-nitrilase-Tm system for the 14 phyla wi
---
height: 700
dataUrls:
- - /rst_rt-nitrilase-tm/Rst_RT-Tm.Rst_RT-Tm__RT-Tm.0.V.pdb
- - /rst_rt-nitrilase-tm/Rst_RT-Tm.Rst_RT-Tm__RT.0.V.pdb
+ - /rst_rt-nitrilase-tm/Rst_RT-Tm.Rst_RT-Tm__RT-Tm.0.V.cif
+ - /rst_rt-nitrilase-tm/Rst_RT-Tm.Rst_RT-Tm__RT.0.V.cif
---
::
diff --git a/content/3.defense-systems/rst_tir-nlr.md b/content/3.defense-systems/rst_tir-nlr.md
index f6df789a..7f2a5457 100644
--- a/content/3.defense-systems/rst_tir-nlr.md
+++ b/content/3.defense-systems/rst_tir-nlr.md
@@ -58,7 +58,7 @@ Proportion of genome encoding the Rst_TIR-NLR system for the 14 phyla with more
---
height: 700
dataUrls:
- - /rst_tir-nlr/Rst_TIR-NLR__TIR.pdb
+ - /rst_tir-nlr/Rst_TIR-NLR__TIR.cif
---
::
diff --git a/content/3.defense-systems/sanata.md b/content/3.defense-systems/sanata.md
index f43723ec..db49c97c 100644
--- a/content/3.defense-systems/sanata.md
+++ b/content/3.defense-systems/sanata.md
@@ -57,8 +57,8 @@ Proportion of genome encoding the SanaTA system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /sanata/SanaTA.SanaTA_SanaA.0.V.pdb
- - /sanata/SanaTA.SanaTA_SanaT.0.V.pdb
+ - /sanata/SanaTA.SanaTA_SanaA.0.V.cif
+ - /sanata/SanaTA.SanaTA_SanaT.0.V.cif
---
::
diff --git a/content/3.defense-systems/sefir.md b/content/3.defense-systems/sefir.md
index 2a75ce4a..d83d29ee 100644
--- a/content/3.defense-systems/sefir.md
+++ b/content/3.defense-systems/sefir.md
@@ -61,7 +61,7 @@ Proportion of genome encoding the SEFIR system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /sefir/SEFIR__bSEFIR.pdb
+ - /sefir/SEFIR__bSEFIR.cif
---
::
diff --git a/content/3.defense-systems/septu.md b/content/3.defense-systems/septu.md
index 2addac55..6ca8108a 100644
--- a/content/3.defense-systems/septu.md
+++ b/content/3.defense-systems/septu.md
@@ -47,8 +47,8 @@ Proportion of genome encoding the Septu system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /septu/Septu.Septu__PtuA.1.V.pdb
- - /septu/Septu.Septu__PtuB.1.V.pdb
+ - /septu/Septu.Septu__PtuA.1.V.cif
+ - /septu/Septu.Septu__PtuB.1.V.cif
---
::
@@ -58,8 +58,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /septu/Septu.Septu__PtuB.1.V.pdb
- - /septu/Septu.Septu__PtuA.1.V.pdb
+ - /septu/Septu.Septu__PtuB.1.V.cif
+ - /septu/Septu.Septu__PtuA.1.V.cif
---
::
diff --git a/content/3.defense-systems/shango.md b/content/3.defense-systems/shango.md
index b174aaf8..a878f553 100644
--- a/content/3.defense-systems/shango.md
+++ b/content/3.defense-systems/shango.md
@@ -58,9 +58,9 @@ Proportion of genome encoding the Shango system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /shango/Shango.Shango__SngA.0.V.pdb
- - /shango/Shango.Shango__SngB.0.V.pdb
- - /shango/Shango.Shango__SngC.0.V.pdb
+ - /shango/Shango.Shango__SngA.0.V.cif
+ - /shango/Shango.Shango__SngB.0.V.cif
+ - /shango/Shango.Shango__SngC.0.V.cif
---
::
diff --git a/content/3.defense-systems/shedu.md b/content/3.defense-systems/shedu.md
index 5835ad1e..fdc8c3d9 100644
--- a/content/3.defense-systems/shedu.md
+++ b/content/3.defense-systems/shedu.md
@@ -62,7 +62,7 @@ Proportion of genome encoding the Shedu system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /shedu/Shedu__SduA.pdb
+ - /shedu/Shedu__SduA.cif
---
::
diff --git a/content/3.defense-systems/shosta.md b/content/3.defense-systems/shosta.md
index 90f1cdd3..6d1e9a31 100644
--- a/content/3.defense-systems/shosta.md
+++ b/content/3.defense-systems/shosta.md
@@ -57,8 +57,8 @@ Proportion of genome encoding the ShosTA system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /shosta/ShosTA.ShosTA__ShosA.0.V.pdb
- - /shosta/ShosTA.ShosTA__ShosT.0.V.pdb
+ - /shosta/ShosTA.ShosTA__ShosA.0.V.cif
+ - /shosta/ShosTA.ShosTA__ShosT.0.V.cif
---
::
diff --git a/content/3.defense-systems/sofic.md b/content/3.defense-systems/sofic.md
index 9b38dbc4..dba25f17 100644
--- a/content/3.defense-systems/sofic.md
+++ b/content/3.defense-systems/sofic.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the SoFIC system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /sofic/SoFic__SoFic.pdb
+ - /sofic/SoFic__SoFic.cif
---
::
diff --git a/content/3.defense-systems/spbk.md b/content/3.defense-systems/spbk.md
index 8b3f25f7..a4a5f0c7 100644
--- a/content/3.defense-systems/spbk.md
+++ b/content/3.defense-systems/spbk.md
@@ -45,7 +45,7 @@ Proportion of genome encoding the SpbK system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /spbk/SpbK__SpbK.pdb
+ - /spbk/SpbK__SpbK.cif
---
::
diff --git a/content/3.defense-systems/sspbcde.md b/content/3.defense-systems/sspbcde.md
index acb6b9bb..2a069f26 100644
--- a/content/3.defense-systems/sspbcde.md
+++ b/content/3.defense-systems/sspbcde.md
@@ -46,10 +46,10 @@ Proportion of genome encoding the SspBCDE system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.pdb
- - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.pdb
- - /sspbcde/SspBCDE.SspBCDE__SspE.0.V.pdb
- - /sspbcde/SspBCDE.SspBCDE__SspB.1.V.pdb
+ - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.cif
+ - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.cif
+ - /sspbcde/SspBCDE.SspBCDE__SspE.0.V.cif
+ - /sspbcde/SspBCDE.SspBCDE__SspB.1.V.cif
---
::
@@ -59,12 +59,12 @@ dataUrls:
---
height: 700
dataUrls:
- - /sspbcde/SspBCDE.SspBCDE__SspH.1.V.pdb
- - /sspbcde/SspBCDE.SspBCDE__SspG.1.V.pdb
- - /sspbcde/SspBCDE.SspBCDE__SspF.1.V.pdb
- - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.pdb
- - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.pdb
- - /sspbcde/SspBCDE.SspBCDE__SspB.1.V.pdb
+ - /sspbcde/SspBCDE.SspBCDE__SspH.1.V.cif
+ - /sspbcde/SspBCDE.SspBCDE__SspG.1.V.cif
+ - /sspbcde/SspBCDE.SspBCDE__SspF.1.V.cif
+ - /sspbcde/SspBCDE.SspBCDE__SspD.0.V.cif
+ - /sspbcde/SspBCDE.SspBCDE__SspC.1.V.cif
+ - /sspbcde/SspBCDE.SspBCDE__SspB.1.V.cif
---
::
diff --git a/content/3.defense-systems/stk2.md b/content/3.defense-systems/stk2.md
index b90aff23..73583cc2 100644
--- a/content/3.defense-systems/stk2.md
+++ b/content/3.defense-systems/stk2.md
@@ -54,7 +54,7 @@ Proportion of genome encoding the Stk2 system for the 14 phyla with more than 50
---
height: 700
dataUrls:
- - /stk2/Stk2__Stk2.pdb
+ - /stk2/Stk2__Stk2.cif
---
::
diff --git a/content/3.defense-systems/thoeris.md b/content/3.defense-systems/thoeris.md
index 37cc0da5..82675885 100644
--- a/content/3.defense-systems/thoeris.md
+++ b/content/3.defense-systems/thoeris.md
@@ -46,8 +46,8 @@ Proportion of genome encoding the Thoeris system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /thoeris/Thoeris_I.Thoeris_I__ThsA_new_grand.0.V.pdb
- - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.pdb
+ - /thoeris/Thoeris_I.Thoeris_I__ThsA_new_grand.0.V.cif
+ - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.cif
---
::
@@ -58,8 +58,8 @@ dataUrls:
---
height: 700
dataUrls:
- - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.pdb
- - /thoeris/Thoeris_II.Thoeris_II__ThsA_new_petit.0.V.pdb
+ - /thoeris/Thoeris_I.Thoeris__ThsB_Global.0.V.cif
+ - /thoeris/Thoeris_II.Thoeris_II__ThsA_new_petit.0.V.cif
---
::
diff --git a/content/3.defense-systems/tiamat.md b/content/3.defense-systems/tiamat.md
index ac0dc63e..e6220d71 100644
--- a/content/3.defense-systems/tiamat.md
+++ b/content/3.defense-systems/tiamat.md
@@ -57,7 +57,7 @@ Proportion of genome encoding the Tiamat system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /tiamat/Tiamat__TmtA.pdb
+ - /tiamat/Tiamat__TmtA.cif
---
::
diff --git a/content/3.defense-systems/uzume.md b/content/3.defense-systems/uzume.md
index eb205809..0944ce2c 100644
--- a/content/3.defense-systems/uzume.md
+++ b/content/3.defense-systems/uzume.md
@@ -44,7 +44,7 @@ Proportion of genome encoding the Uzume system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /uzume/Uzume__UzmA.pdb
+ - /uzume/Uzume__UzmA.cif
---
::
diff --git a/content/3.defense-systems/viperin.md b/content/3.defense-systems/viperin.md
index 9248671f..d02242bd 100644
--- a/content/3.defense-systems/viperin.md
+++ b/content/3.defense-systems/viperin.md
@@ -64,7 +64,7 @@ Proportion of genome encoding the Viperin system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /viperin/Viperin__pVip.pdb
+ - /viperin/Viperin__pVip.cif
---
::
diff --git a/content/3.defense-systems/wadjet.md b/content/3.defense-systems/wadjet.md
index a4c099ba..022dbdc1 100644
--- a/content/3.defense-systems/wadjet.md
+++ b/content/3.defense-systems/wadjet.md
@@ -53,10 +53,10 @@ Proportion of genome encoding the Wadjet system for the 14 phyla with more than
---
height: 700
dataUrls:
- - /wadjet/Wadjet_I.Wadjet__JetA_I.0.V.pdb
- - /wadjet/Wadjet_I.Wadjet__JetB_I.0.V.pdb
- - /wadjet/Wadjet_I.Wadjet__JetC_I.0.V.pdb
- - /wadjet/Wadjet_I.Wadjet__JetD_I.0.V.pdb
+ - /wadjet/Wadjet_I.Wadjet__JetA_I.0.V.cif
+ - /wadjet/Wadjet_I.Wadjet__JetB_I.0.V.cif
+ - /wadjet/Wadjet_I.Wadjet__JetC_I.0.V.cif
+ - /wadjet/Wadjet_I.Wadjet__JetD_I.0.V.cif
---
::
@@ -67,10 +67,10 @@ dataUrls:
---
height: 700
dataUrls:
- - /wadjet/Wadjet_II.Wadjet__JetD_II.0.V.pdb
- - /wadjet/Wadjet_II.Wadjet__JetC_II.0.V.pdb
- - /wadjet/Wadjet_II.Wadjet__JetB_II.0.V.pdb
- - /wadjet/Wadjet_II.Wadjet__JetA_II.0.V.pdb
+ - /wadjet/Wadjet_II.Wadjet__JetD_II.0.V.cif
+ - /wadjet/Wadjet_II.Wadjet__JetC_II.0.V.cif
+ - /wadjet/Wadjet_II.Wadjet__JetB_II.0.V.cif
+ - /wadjet/Wadjet_II.Wadjet__JetA_II.0.V.cif
---
::
@@ -81,10 +81,10 @@ dataUrls:
---
height: 700
dataUrls:
- - /wadjet/Wadjet_III.Wadjet__JetD_III.0.V.pdb
- - /wadjet/Wadjet_III.Wadjet__JetA_III.0.V.pdb
- - /wadjet/Wadjet_III.Wadjet__JetB_III.0.V.pdb
- - /wadjet/Wadjet_III.Wadjet__JetC_III.0.V.pdb
+ - /wadjet/Wadjet_III.Wadjet__JetD_III.0.V.cif
+ - /wadjet/Wadjet_III.Wadjet__JetA_III.0.V.cif
+ - /wadjet/Wadjet_III.Wadjet__JetB_III.0.V.cif
+ - /wadjet/Wadjet_III.Wadjet__JetC_III.0.V.cif
---
::
diff --git a/content/3.defense-systems/zorya.md b/content/3.defense-systems/zorya.md
index a83c1d3c..17d9ebd5 100644
--- a/content/3.defense-systems/zorya.md
+++ b/content/3.defense-systems/zorya.md
@@ -50,10 +50,10 @@ Proportion of genome encoding the Zorya system for the 14 phyla with more than 5
---
height: 700
dataUrls:
- - /zorya/Zorya_TypeI.Zorya_TypeI__ZorC.0.V.pdb
- - /zorya/Zorya_TypeI.Zorya_TypeI__ZorD.0.V.pdb
- - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.pdb
- - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.pdb
+ - /zorya/Zorya_TypeI.Zorya_TypeI__ZorC.0.V.cif
+ - /zorya/Zorya_TypeI.Zorya_TypeI__ZorD.0.V.cif
+ - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.cif
+ - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.cif
---
::
@@ -64,9 +64,9 @@ dataUrls:
---
height: 700
dataUrls:
- - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.pdb
- - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.pdb
- - /zorya/Zorya_TypeII.Zorya_TypeII__ZorE.0.V.pdb
+ - /zorya/Zorya_TypeII.Zorya__ZorA.0.V.cif
+ - /zorya/Zorya_TypeI.Zorya__ZorB.0.V.cif
+ - /zorya/Zorya_TypeII.Zorya_TypeII__ZorE.0.V.cif
---
::
--
GitLab