content/3.defense-systems/pd-t4-2.md

@@ -10,6 +10,8 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF03235, PF18735
+relevantAbstracts:
+    - doi: 10.1038/s41564-022-01219-4
 ---
 
 # PD-T4-2
@@ -34,25 +36,23 @@ The system was detected in 28 different species.
 Proportion of genome encoding the PD-T4-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T4-2
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t4-2/PD-T4-2,PD-T4-2__PD-T4-2_A,0,DF-plddts_90.58136.pdb
----
-::
+dataUrls:
+   - /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
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t4-2/PD-T4-2,PD-T4-2__PD-T4-2_B,0,DF-plddts_93.48773.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -79,13 +79,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1038/s41564-022-01219-4
-
----
-::
 

content/3.defense-systems/pd-t4-3.md

@@ -46,18 +46,22 @@ The system was detected in 172 different species.
 Proportion of genome encoding the PD-T4-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T4-3
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t4-3/PD-T4-3__PD-T4-3-plddts_88.02514.pdb
+dataUrls:
+   - /pd-t4-3/PD-T4-3__PD-T4-3.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -85,3 +89,4 @@ end
 </mermaid>
 ---
 ::
+

content/3.defense-systems/pd-t4-4.md

@@ -44,25 +44,23 @@ The system was detected in 37 different species.
 Proportion of genome encoding the PD-T4-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T4-4
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t4-4/PD-T4-4,PD-T4-4__PD-T4-4_A,0,V-plddts_89.6125.pdb
----
-::
+dataUrls:
+   - /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
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t4-4/PD-T4-4,PD-T4-4__PD-T4-4_B,0,V-plddts_92.18973.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -90,3 +88,4 @@ end
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
 
+

content/3.defense-systems/pd-t4-5.md

@@ -10,6 +10,8 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF07751
+relevantAbstracts:
+    - doi: 10.1038/s41564-022-01219-4
 ---
 
 # PD-T4-5
@@ -34,18 +36,22 @@ The system was detected in 128 different species.
 Proportion of genome encoding the PD-T4-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T4-5
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t4-5/PD-T4-5__PD-T4-5-plddts_94.58803.pdb
+dataUrls:
+   - /pd-t4-5/PD-T4-5__PD-T4-5.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -72,13 +78,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1038/s41564-022-01219-4
-
----
-::
 

content/3.defense-systems/pd-t4-6.md

@@ -45,18 +45,22 @@ The system was detected in 18 different species.
 Proportion of genome encoding the PD-T4-6 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T4-6
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t4-6/PD-T4-6__PD-T4-6-plddts_84.95824.pdb
+dataUrls:
+   - /pd-t4-6/PD-T4-6__PD-T4-6.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -82,3 +86,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/pd-t4-7.md

@@ -47,18 +47,22 @@ The system was detected in 100 different species.
 Proportion of genome encoding the PD-T4-7 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T4-7
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t4-7/PD-T4-7__PD-T4-7-plddts_91.28596.pdb
+dataUrls:
+   - /pd-t4-7/PD-T4-7__PD-T4-7.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -84,3 +88,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/pd-t4-8.md

@@ -45,18 +45,22 @@ The system was detected in 50 different species.
 Proportion of genome encoding the PD-T4-8 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T4-8
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t4-8/PD-T4-8__PD-T4-8-plddts_91.39016.pdb
+dataUrls:
+   - /pd-t4-8/PD-T4-8__PD-T4-8.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -84,3 +88,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/pd-t4-9.md

@@ -10,6 +10,8 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF02556
+relevantAbstracts:
+    - doi: 10.1038/s41564-022-01219-4
 ---
 
 # PD-T4-9
@@ -34,32 +36,24 @@ The system was detected in 88 different species.
 Proportion of genome encoding the PD-T4-9 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T4-9
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t4-9/PD-T4-9,PD-T4-9__PD-T4-9_A,0,V-plddts_93.71807.pdb
----
-::
+dataUrls:
+   - /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
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t4-9/PD-T4-9,PD-T4-9__PD-T4-9_B,0,V-plddts_71.02357.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t4-9/PD-T4-9,PD-T4-9__PD-T4-9_C,0,V-plddts_93.05735.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -86,13 +80,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1038/s41564-022-01219-4
-
----
-::
 

content/3.defense-systems/pd-t7-1.md

@@ -9,6 +9,8 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+relevantAbstracts:
+    - doi: 10.1038/s41564-022-01219-4
 ---
 
 # PD-T7-1
@@ -33,18 +35,22 @@ The system was detected in 146 different species.
 Proportion of genome encoding the PD-T7-1 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T7-1
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t7-1/PD-T7-1__PD-T7-1-plddts_93.91174.pdb
+dataUrls:
+   - /pd-t7-1/PD-T7-1__PD-T7-1.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -68,12 +74,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
 
-::relevant-abstracts
----
-items:
-    - doi: 10.1038/s41564-022-01219-4
-
----
-::

content/3.defense-systems/pd-t7-2.md

@@ -10,6 +10,8 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF01935, PF13289
+relevantAbstracts:
+    - doi: 10.1038/s41564-022-01219-4
 ---
 
 # PD-T7-2
@@ -34,25 +36,23 @@ The system was detected in 667 different species.
 Proportion of genome encoding the PD-T7-2 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T7-2
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t7-2/PD-T7-2,PD-T7-2__PD-T7-2_A,0,V-plddts_90.8134.pdb
----
-::
+dataUrls:
+   - /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
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pd-t7-2/PD-T7-2,PD-T7-2__PD-T7-2_B,0,V-plddts_86.88934.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -84,13 +84,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1038/s41564-022-01219-4
-
----
-::
 

content/3.defense-systems/pd-t7-3.md

@@ -45,18 +45,22 @@ The system was detected in 130 different species.
 Proportion of genome encoding the PD-T7-3 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T7-3
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t7-3/PD-T7-3__PD-T7-3-plddts_89.74752.pdb
+dataUrls:
+   - /pd-t7-3/PD-T7-3__PD-T7-3.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -87,3 +91,4 @@ end
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
 
+

content/3.defense-systems/pd-t7-4.md

@@ -10,6 +10,8 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF13643
+relevantAbstracts:
+    - doi: 10.1038/s41564-022-01219-4
 ---
 
 # PD-T7-4
@@ -34,18 +36,22 @@ The system was detected in 218 different species.
 Proportion of genome encoding the PD-T7-4 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T7-4
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t7-4/PD-T7-4__PD-T7-4-plddts_93.28251.pdb
+dataUrls:
+   - /pd-t7-4/PD-T7-4__PD-T7-4.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -72,13 +78,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1038/s41564-022-01219-4
-
----
-::
 

content/3.defense-systems/pd-t7-5.md

@@ -9,6 +9,8 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+relevantAbstracts:
+    - doi: 10.1038/s41564-022-01219-4
 ---
 
 # PD-T7-5
@@ -33,18 +35,22 @@ The system was detected in 129 different species.
 Proportion of genome encoding the PD-T7-5 system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PD-T7-5
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pd-t7-5/PD-T7-5__PD-T7-5-plddts_92.01228.pdb
+dataUrls:
+   - /pd-t7-5/PD-T7-5__PD-T7-5.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Vassallo_2022[<a href='https://doi.org/10.1038/s41564-022-01219-4'>Vassallo et al., 2022</a>] --> Origin_0
@@ -70,12 +76,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
 
-::relevant-abstracts
----
-items:
-    - doi: 10.1038/s41564-022-01219-4
-
----
-::

content/3.defense-systems/pfiat.md

@@ -10,6 +10,8 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF02604, PF05016
+relevantAbstracts:
+    - doi: 10.1111/1751-7915.13570
 ---
 
 # PfiAT
@@ -34,31 +36,17 @@ The system was detected in 308 different species.
 Proportion of genome encoding the PfiAT system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PfiAT
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pfiat/PfiAT,PfiAT__PfiA,0,V-plddts_95.62475.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pfiat/PfiAT,PfiAT__PfiT,0,V-plddts_94.1034.pdb
----
-::
-
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1111/1751-7915.13570
+dataUrls:
+   - /pfiat/PfiAT.PfiAT__PfiA.0.V.cif
+   - /pfiat/PfiAT.PfiAT__PfiT.0.V.cif
 
 ---
 ::
-

content/3.defense-systems/pif.md

@@ -50,25 +50,23 @@ The system was detected in 25 different species.
 Proportion of genome encoding the Pif system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Pif
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pif/Pif,Pif__PifA,0,V-plddts_83.95828.pdb
----
-::
+dataUrls:
+   - /pif/Pif.Pif__PifA.0.V.cif
+   - /pif/Pif.Pif__PifC.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pif/Pif,Pif__PifC,0,V-plddts_91.50188.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Cheng_2004[<a href='https://doi.org/10.1016/j.virol.2004.06.001'>Cheng et al., 2004</a>] --> Origin_0
@@ -92,3 +90,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/prrc.md

@@ -50,25 +50,35 @@ The system was detected in 309 different species.
 Proportion of genome encoding the PrrC system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PrrC
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /prrc/PrrC__EcoprrI-plddts_91.30003.pdb
+dataUrls:
+   - /prrc/PrrC__EcoprrI.cif
+   - /prrc/PrrC__PrrC.cif
+
 ---
 ::
+### RM
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /prrc/PrrC__PrrC-plddts_86.4815.pdb
+dataUrls:
+   - /prrc/RM__Type_I_S.cif
+   - /prrc/RM__Type_I_REases.cif
+
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Jabbar_1984[<a href='https://doi.org/10.1128/JVI.51.2.522-529.1984'>Jabbar and  Snyder, 1984</a>] --> Origin_0
@@ -95,3 +105,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/psyrta.md

@@ -66,25 +66,23 @@ The system was detected in 132 different species.
 Proportion of genome encoding the PsyrTA system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### PsyrTA
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /psyrta/PsyrTA,PsyrTA__PsyrA,0,V-plddts_88.4921.pdb
----
-::
+dataUrls:
+   - /psyrta/PsyrTA.PsyrTA__PsyrT.0.V.cif
+   - /psyrta/PsyrTA.PsyrTA__PsyrA.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /psyrta/PsyrTA,PsyrTA__PsyrT,0,V-plddts_88.00999.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Millman_2022[<a href='https://doi.org/10.1016/j.chom.2022.09.017'>Millman et al., 2022</a>] --> Origin_0
@@ -112,3 +110,4 @@ end
 </mermaid>
 ::
 
+

content/3.defense-systems/pycsar.md

@@ -10,6 +10,8 @@ tableColumns:
     Activator: Signaling molecules
     Effector: Membrane disrupting, Nucleotides modifying
     PFAM: PF00004, PF00027, PF00211, PF00899, PF01734, PF10137, PF14461, PF14464, PF18145, PF18153, PF18303, PF18967
+relevantAbstracts:
+    - doi: 10.1016/j.cell.2021.09.031
 ---
 
 # Pycsar
@@ -36,41 +38,34 @@ The system was detected in 295 different species.
 Proportion of genome encoding the Pycsar system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
+## Structure
 ### Pycsar
+##### Example 1
 
-Example 1:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pycsar/Pycsar,CBASS__TIR,0,V-plddts_90.36719.pdb
----
-::
+dataUrls:
+   - /pycsar/Pycsar.Pycsar__AG_cyclase.1.V.cif
+   - /pycsar/Pycsar.CBASS__TIR.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pycsar/Pycsar,Pycsar__AG_cyclase,0,V-plddts_94.90778.pdb
 ---
 ::
+##### Example 2
 
-Example 2:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /pycsar/Pycsar,CBASS__TIR,0,V-plddts_90.36719.pdb
----
-::
+dataUrls:
+   - /pycsar/Pycsar.CBASS_TM.1.V.cif
+   - /pycsar/Pycsar.Pycsar__AG_cyclase.1.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /pycsar/Pycsar,Pycsar__AG_cyclase,0,V-plddts_94.90778.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Tal_2021[<a href='https://doi.org/10.1016/j.cell.2021.09.031'>Tal et al., 2021</a>] --> Origin_0
@@ -104,13 +99,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1016/j.cell.2021.09.031
-
----
-::
 

content/3.defense-systems/radar.md

@@ -9,7 +9,6 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Nucleic acid degrading
-
 contributors: 
   - Hugo Vaysset
   - Aude Bernheim
@@ -54,41 +53,31 @@ The system was detected in 44 different species.
 Proportion of genome encoding the RADAR system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
+
 ## Structure
 
-### Experimentaly determined structure
+### Experimentally determined structure
 
 From :ref{doi=10.1016/j.cell.2023.01.012} in *Escherichia coli*:
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /radar/8fnt_EcRdrA_7mer.pdb
----
-::
-
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/8fnv_EcRdrB_12mer.pdb
+dataUrls: 
+    - /radar/8fnt_EcRdrA_7mer.pdb
+    - /radar/8fnv_EcRdrB_12mer.pdb
+    - /radar/8fnw_EcRdrAB_7_12mer.cif
 ---
 ::
 
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/8fnw_EcRdrAB_7_12mer.cif
----
-::
-
 From :ref{doi=10.1016/j.cell.2023.01.012} in *Streptococcus suis*:
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /radar/8fnu_SsRdrA_7mer.pdb
+dataUrls: 
+    - /radar/8fnu_SsRdrA_7mer.pdb
 ---
 ::
 
@@ -97,85 +86,44 @@ From :ref{doi=10.1016/j.cell.2023.01.026} in *Escherichia coli*:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /radar/8hr8_EcRdrA_7mer.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/8hr9_EcRdrA_14mer.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/8hrc_EcRdrB_12mer.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/8hr7_EcRdrAB_7_12mer.cif
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/8hra_EcRdrA_7mer_rna.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/8hrb_EcRdrA_14mer_rna.pdb
+dataUrls: 
+    - /radar/8hr8_EcRdrA_7mer.pdb
+    - /radar/8hr9_EcRdrA_14mer.pdb
+    - /radar/8hrc_EcRdrB_12mer.pdb
+    - /radar/8hr7_EcRdrAB_7_12mer.cif
+    - /radar/8hra_EcRdrA_7mer_rna.pdb
+    - /radar/8hrb_EcRdrA_14mer_rna.pdb
 ---
 ::
 
 ### radar_I
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /radar/radar_I,radar_I__rdrA_I,0,V-plddts_84.65854.pdb
----
-::
+dataUrls:
+   - /radar/radar_I.radar_I__rdrB_I.0.V.cif
+   - /radar/radar_I.radar_I__rdrA_I.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/radar_I,radar_I__rdrB_I,0,V-plddts_87.10562.pdb
 ---
 ::
-
 ### radar_II
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /radar/radar_II,radar_II__rdrA_II,0,V-plddts_84.35322.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/radar_II,radar_II__rdrB_II,0,V-plddts_86.83828.pdb
----
-::
+dataUrls:
+   - /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
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /radar/radar_II,radar_II__rdrC_II,0,V-plddts_75.42507.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -231,3 +179,4 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+

content/3.defense-systems/retron.md

@@ -123,205 +123,143 @@ The system was detected in 840 different species.
 Proportion of genome encoding the Retron system for the 14 phyla with more than 50 genomes in the RefSeq database.
 
 
-## Structure
 
-### Retron_II
+## Structure
+### RT_Ec67_SLATT
+##### Example Ec57
 
-Example 1:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_II,Retron_II__NDT,Ec73,V-plddts_91.19742.pdb
----
-::
+dataUrls:
+   - /retron/RT_Ec67_SLATT.AbiA__AbiA_small_SLATT.Ec57.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_II,Retron__RT_Tot,Ec73,V-plddts_94.26558.pdb
 ---
 ::
+##### Example Ec67
 
-Example 2:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_II,Retron_II__NDT,Ec73,V-plddts_91.19742.pdb
----
-::
+dataUrls:
+   - /retron/DRT_3.DRT_3__drt3a.0.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_II,Retron__RT_Tot,Ec73,V-plddts_94.26558.pdb
 ---
 ::
+### Retron_II
+##### Example Ec73
 
-### Retron_III
-
-Example 1:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_III,Retron_III__PRTase,0,DF-plddts_93.05385.pdb
----
-::
+dataUrls:
+   - /retron/Retron_II.Retron_II__NDT.Ec73.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_III,Retron_III__WH,0,DF-plddts_81.40731.pdb
 ---
 ::
+##### Example Ec86
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_III,Retron__RT_Tot,0,DF-plddts_95.80558.pdb
----
-::
+dataUrls:
+   - /retron/Retron_II.Retron_II__NDT.Ec73.V.cif
 
-Example 2:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_III,Retron_III__PRTase,0,DF-plddts_93.05385.pdb
 ---
 ::
+### Retron_III
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_III,Retron_III__WH,0,DF-plddts_81.40731.pdb
----
-::
+dataUrls:
+   - /retron/Retron_III.Retron_III__PRTase.0.DF.cif
+   - /retron/Retron_III.Retron_III__WH.0.DF.cif
 
-### Retron_IV
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_IV,Retron_IV__2TM,Ec48,V-plddts_90.18352.pdb
 ---
 ::
+##### Example 2
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_IV,Retron__RT_Tot,Ec48,V-plddts_92.96552.pdb
----
-::
-
-### Retron_I_A
+dataUrls:
+   - /retron/Retron_III.Retron_III__PRTase_WH.1.DF.cif
 
-Example 1:
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec78.V-plddts_94.92113.pdb
 ---
 ::
+### Retron_IV
+##### Example Ec48
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec83.V-plddts_95.89569.pdb
----
-::
+dataUrls:
+   - /retron/Retron_IV.Retron_IV__2TM.Ec48.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Vc95.V-plddts_96.13478.pdb
 ---
 ::
+### Retron_I_A
+##### Example Ec83
 
-Example 2:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec78.V-plddts_94.92113.pdb
----
-::
+dataUrls:
+   - /retron/Retron_I_A.Retron__RT_Tot.Ec83.V.cif
+   - /retron/Retron_I_A.Retron_I_A__ATPase_TypeIA.Vc95.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec83.V-plddts_95.89569.pdb
 ---
 ::
+##### Example Vc95
 
-Example 3:
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec78.V-plddts_94.92113.pdb
----
-::
+dataUrls:
+   - /retron/Retron_I_A.Retron_I_A__ATPase_TypeIA.Vc95.V.cif
+   - /retron/Retron_I_A.Retron__RT_Tot.Ec83.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_I_A.Retron_I_A__HNH_TIGR02646.Ec83.V-plddts_95.89569.pdb
 ---
 ::
-
 ### Retron_I_B
+##### Example Eco8
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_I_B,Retron_I_B__ATPase_TOPRIM_COG3593,Eco8,V-plddts_86.92789.pdb
----
-::
+dataUrls:
+   - /retron/Retron_I_B.Retron_I_B__ATPase_TOPRIM_COG3593.Eco8.V.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_I_B,Retron__RT_Tot,Eco8,V-plddts_93.00774.pdb
 ---
 ::
-
 ### Retron_VI
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_VI,Possible_Retron_VI__SP,0,DF-plddts_81.90355.pdb
----
-::
+dataUrls:
+   - /retron/Retron_VI.Retron_VI__HTH.0.DF.cif
+   - /retron/Retron_VI.Possible_Retron_VI__SP.0.DF.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_VI,Retron_VI__HTH,0,DF-plddts_86.36271.pdb
 ---
 ::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_VI,Retron__RT_Tot,0,DF-plddts_95.37927.pdb
----
-::
-
 ### Retron_VII_2
+##### Example 1
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /retron/Retron_VII_2,Retron_VII_2__DUF3800,0,DF-plddts_91.55254.pdb
----
-::
+dataUrls:
+   - /retron/Retron_VII_2.Retron_VII_2__DUF3800.0.DF.cif
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /retron/Retron_VII_2,Retron__RT_Tot,0,DF-plddts_95.60845.pdb
 ---
 ::
 
 ## Experimental validation
+
 <mermaid>
 graph LR;
     Fillol-Salom_2022[<a href='https://doi.org/10.1016/j.cell.2022.07.014'>Fillol-Salom et al., 2022</a>] --> Origin_0
@@ -566,3 +504,4 @@ end
 </mermaid>
 
 
+