Compare revisions

Jean CURY · Remi PLANEL · Remi PLANEL · Jean c · Remi PLANEL · Jean CURY
--- a/components/content/MolstarPdbePlugin.vue
+++ b/components/content/MolstarPdbePlugin.vue
@@ -107,7 +107,7 @@ const pdbeMolstarComponent = ref(null)
 const selectedPdb: Ref<string | null> = ref(null)
 const structureToDownload: Ref<string | null> = ref(null)
 const selectedPaePath = computed(() => {
-    return selectedPdb.value ? `${selectedPdb.value.split(".").slice(0, -1).join('.')}.png` : null
+    return selectedPdb.value ? `${selectedPdb.value.split(".").slice(0, -1).join('.')}.png` : undefined
 })

 watch(selectedPdb, (newSelectedPdb, prevSelectPdb) => {
@@ -190,10 +190,9 @@ const moleculeFormat: Ref<string> = ref("pdb")
                    <v-col :cols="mobile ? 12 : 'auto'">
                        <v-sheet v-if="selectedPdb"
                            class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3"
-                            :height="computedHeight" :width="computedWidth" position="relative">
-                            <pdbe-molstar ref="pdbeMolstarComponent" landscape="true" hide-controls="true"
-                                :custom-data-url="selectedPdb" alphafold-view="true"
-                                :custom-data-format="moleculeFormat"></pdbe-molstar>
+                            :height="computedHeight" :width="computedWidth" style="position:relative;">
+                            <pdbe-molstar ref="pdbeMolstarComponent" :custom-data-url="selectedPdb" alphafold-view
+                                sequence-panel="true" landscape="false" :custom-data-format="moleculeFormat"></pdbe-molstar>
                        </v-sheet>
                    </v-col>
                    <v-col :cols="mobile ? 12 : undefined">
@@ -272,4 +271,4 @@ div.msp-plugin-content.msp-layout-expanded {
    height: 16px;
    width: 16px;
 }
-</style>
\ No newline at end of file
+</style>
--- a/components/content/StructureDb.vue
+++ b/components/content/StructureDb.vue
@@ -8,7 +8,8 @@ import { useNumericalFilter } from "@/composables/useNumericalfilter"
 import { ServerDbTable } from "#components"
 const sortBy: Ref<SortItem[]> = ref([{ key: 'System', order: "asc" }])
 const itemValue = ref("id");
-const facets: Ref<string[]> = ref(["System", "subtype", "gene_name", "completed", "prediction_type",])
+const facets: Ref<string[]> = ref(["System", "subtype", "gene_name", "completed", "prediction_type", "proteins_in_the_prediction", "system_genes",
+])
 const headers: Ref<Object[]> = ref([
    { title: 'Structure', key: 'structure', sortable: false, removable: false },
    { title: "System", key: "System", removable: false },

--- a/content/3.defense-systems/abia.md
+++ b/content/3.defense-systems/abia.md
@@ -44,35 +44,35 @@ The system was detected in 35 different species.
 Proportion of genome encoding the AbiA system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiA_large
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abia/AbiA_large__AbiA_large-plddts_90.82916.pdb
+dataUrls:
+   - /abia/AbiA_large__AbiA_large.cif
+
 ---
 ::
-
 ### AbiA_small
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abia/AbiA_small,AbiA_small__AbiA_SLATT,0,DF-plddts_94.13374.pdb
---
-::
+dataUrls:
+   - /abia/AbiA_small.AbiA_small__AbiA_small.0.DF.cif
+   - /abia/AbiA_small.AbiA_small__AbiA_SLATT.0.DF.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /abia/AbiA_small,AbiA_small__AbiA_small,0,DF-plddts_89.82347.pdb
 ---
 ::

 ## Experimental validation

+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -98,3 +98,4 @@ end
    style Title3 fill:none,stroke:none,stroke-width:none
    style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
+
--- a/content/3.defense-systems/abib.md
+++ b/content/3.defense-systems/abib.md
@@ -47,18 +47,22 @@ The system was detected in 5 different species.
 Proportion of genome encoding the AbiB system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiB
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abib/AbiB__AbiB-plddts_74.5545.pdb
+dataUrls:
+   - /abib/AbiB__AbiB.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -84,3 +88,4 @@ end
 </mermaid>


+
--- a/content/3.defense-systems/abic.md
+++ b/content/3.defense-systems/abic.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF16872
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
 ---

 # AbiC
@@ -35,18 +38,22 @@ The system was detected in 57 different species.
 Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiC
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abic/AbiC__AbiC-plddts_83.80335.pdb
+dataUrls:
+   - /abic/AbiC__AbiC.cif
+
 ---
 ::

 ## 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
@@ -102,14 +109,4 @@ 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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-
---
-::

--- a/content/3.defense-systems/abid.md
+++ b/content/3.defense-systems/abid.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF07751
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
 ---

 # AbiD
@@ -35,18 +38,22 @@ The system was detected in 964 different species.
 Proportion of genome encoding the AbiD system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiD
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abid/AbiD__AbiD-plddts_91.87407.pdb
+dataUrls:
+   - /abid/AbiD__AbiD.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -72,14 +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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-
---
-::

--- a/content/3.defense-systems/abie.md
+++ b/content/3.defense-systems/abie.md
@@ -10,6 +10,10 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF08843, PF09407, PF09952, PF11459, PF13338, PF17194
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1093/nar/gkt1419
 ---

 # AbiE
@@ -44,25 +48,23 @@ The system was detected in 1107 different species.
 Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiE
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abie/AbiE,AbiE__AbiEi,0,V-plddts_85.81224.pdb
---
-::
+dataUrls:
+   - /abie/AbiE.AbiE__AbiEi.0.V.cif
+   - /abie/AbiE.AbiE__AbiEii.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /abie/AbiE,AbiE__AbiEii,0,V-plddts_90.73768.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -86,15 +88,4 @@ 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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-    - doi: 10.1093/nar/gkt1419
-
---
-::

--- a/content/3.defense-systems/abig.md
+++ b/content/3.defense-systems/abig.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF10899, PF16873
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
 ---

 # AbiG
@@ -35,25 +38,23 @@ The system was detected in 22 different species.
 Proportion of genome encoding the AbiG system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiG
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abig/AbiG,AbiG__AbiGi,0,V-plddts_92.08021.pdb
---
-::
+dataUrls:
+   - /abig/AbiG.AbiG__AbiGi.0.V.cif
+   - /abig/AbiG.AbiG__AbiGii.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /abig/AbiG,AbiG__AbiGii,0,V-plddts_88.01846.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -79,14 +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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-
---
-::

--- a/content/3.defense-systems/abih.md
+++ b/content/3.defense-systems/abih.md
@@ -46,18 +46,22 @@ The system was detected in 439 different species.
 Proportion of genome encoding the AbiH system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiH
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abih/AbiH__AbiH-plddts_91.3485.pdb
+dataUrls:
+   - /abih/AbiH__AbiH.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -85,3 +89,4 @@ end



+
--- a/content/3.defense-systems/abii.md
+++ b/content/3.defense-systems/abii.md
@@ -9,6 +9,9 @@ tableColumns:
    Sensor: Unknown
    Activator: Unknown
    Effector: Unknown
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
 ---

 # AbiI
@@ -33,18 +36,22 @@ The system was detected in 6 different species.
 Proportion of genome encoding the AbiI system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiI
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abii/AbiI__AbiI-plddts_90.31131.pdb
+dataUrls:
+   - /abii/AbiI__AbiI.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -69,13 +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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-
---
-::
--- a/content/3.defense-systems/abij.md
+++ b/content/3.defense-systems/abij.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF14355
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
 ---

 # AbiJ
@@ -34,18 +37,22 @@ The system was detected in 261 different species.
 Proportion of genome encoding the AbiJ system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiJ
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abij/AbiJ__AbiJ-plddts_85.12535.pdb
+dataUrls:
+   - /abij/AbiJ__AbiJ.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -69,14 +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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-
---
-::

--- a/content/3.defense-systems/abik.md
+++ b/content/3.defense-systems/abik.md
@@ -10,6 +10,10 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF00078
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1093/nar/gkac467
 ---

 # AbiK
@@ -34,18 +38,22 @@ The system was detected in 32 different species.
 Proportion of genome encoding the AbiK system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiK
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abik/AbiK__AbiK-plddts_91.42521.pdb
+dataUrls:
+   - /abik/AbiK__AbiK.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -71,15 +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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-    - doi: 10.1093/nar/gkac467
-
---
-::

--- a/content/3.defense-systems/abil.md
+++ b/content/3.defense-systems/abil.md
@@ -49,25 +49,23 @@ The system was detected in 126 different species.
 Proportion of genome encoding the AbiL system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiL
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abil/AbiL,AbiL__AbiLi,0,V-plddts_89.17612.pdb
---
-::
+dataUrls:
+   - /abil/AbiL.AbiL__AbiLi.0.V.cif
+   - /abil/AbiL.AbiL__AbiLii.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /abil/AbiL,AbiL__AbiLii,0,V-plddts_86.69766.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -95,3 +93,4 @@ end



+
--- a/content/3.defense-systems/abin.md
+++ b/content/3.defense-systems/abin.md
@@ -9,6 +9,9 @@ tableColumns:
    Sensor: Unknown
    Activator: Unknown
    Effector: Unknown
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
 ---

 # AbiN
@@ -33,18 +36,22 @@ The system was detected in 52 different species.
 Proportion of genome encoding the AbiN system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiN
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abin/AbiN__AbiN-plddts_84.27216.pdb
+dataUrls:
+   - /abin/AbiN__AbiN.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -69,13 +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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-
---
-::
--- a/content/3.defense-systems/abio.md
+++ b/content/3.defense-systems/abio.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF01443, PF09848
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
 ---

 # AbiO
@@ -34,18 +37,22 @@ The system was detected in 61 different species.
 Proportion of genome encoding the AbiO system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiO
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abio/AbiO__AbiO-plddts_87.43501.pdb
+dataUrls:
+   - /abio/AbiO__AbiO.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -70,14 +77,4 @@ 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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-
---
-::

--- a/content/3.defense-systems/abip2.md
+++ b/content/3.defense-systems/abip2.md
@@ -10,6 +10,10 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF00078
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1093/nar/gkac467
 ---

 # AbiP2
@@ -34,18 +38,22 @@ The system was detected in 96 different species.
 Proportion of genome encoding the AbiP2 system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiP2
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abip2/AbiP2__AbiP2-plddts_93.08218.pdb
+dataUrls:
+   - /abip2/AbiP2__AbiP2.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Gao_2020[<a href='https://doi.org/10.1126/science.aba0372'>Gao et al., 2020</a>] --> Origin_0
@@ -78,15 +86,4 @@ 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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-    - doi: 10.1093/nar/gkac467
-
---
-::

--- a/content/3.defense-systems/abiq.md
+++ b/content/3.defense-systems/abiq.md
@@ -10,6 +10,10 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF13958
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
+    - doi: 10.1128/AEM.64.12.4748-4756.1998
 ---

 # AbiQ
@@ -34,18 +38,22 @@ The system was detected in 111 different species.
 Proportion of genome encoding the AbiQ system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiQ
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abiq/AbiQ__AbiQ-plddts_90.84212.pdb
+dataUrls:
+   - /abiq/AbiQ__AbiQ.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -70,15 +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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-    - doi: 10.1128/AEM.64.12.4748-4756.1998
-
---
-::

--- a/content/3.defense-systems/abir.md
+++ b/content/3.defense-systems/abir.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF00176, PF00271, PF04545, PF04851, PF13091
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
 ---

 # AbiR
@@ -34,32 +37,24 @@ The system was detected in 28 different species.
 Proportion of genome encoding the AbiR system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiR
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abir/AbiR,AbiR__AbiRa,0,V-plddts_88.45598.pdb
---
-::
+dataUrls:
+   - /abir/AbiR.AbiR__AbiRc.0.V.cif
+   - /abir/AbiR.AbiR__AbiRb.0.V.cif
+   - /abir/AbiR.AbiR__AbiRa.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /abir/AbiR,AbiR__AbiRb,0,V-plddts_92.82829.pdb
---
-::
-
-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /abir/AbiR,AbiR__AbiRc,0,V-plddts_86.60767.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -84,14 +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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-
---
-::

--- a/content/3.defense-systems/abit.md
+++ b/content/3.defense-systems/abit.md
@@ -10,6 +10,9 @@ tableColumns:
    Activator: Unknown
    Effector: Unknown
    PFAM: PF18864
+relevantAbstracts:
+    - doi: 10.1023/A:1002027321171
+    - doi: 10.1016/j.mib.2005.06.006
 ---

 # AbiT
@@ -34,25 +37,23 @@ The system was detected in 6 different species.
 Proportion of genome encoding the AbiT system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiT
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abit/AbiT,AbiT__AbiTi,0,V-plddts_81.84478.pdb
---
-::
+dataUrls:
+   - /abit/AbiT.AbiT__AbiTi.0.V.cif
+   - /abit/AbiT.AbiT__AbiTii.0.V.cif

-::molstar-pdbe-plugin
---
-height: 700
-dataUrl: /abit/AbiT,AbiT__AbiTii,0,V-plddts_88.46375.pdb
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</a>] --> Origin_0
@@ -77,14 +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: 10.1023/A:1002027321171
-    - doi: 10.1016/j.mib.2005.06.006
-
---
-::

--- a/content/3.defense-systems/abiu.md
+++ b/content/3.defense-systems/abiu.md
@@ -47,18 +47,22 @@ The system was detected in 389 different species.
 Proportion of genome encoding the AbiU system for the 14 phyla with more than 50 genomes in the RefSeq database.


-## Structure

+## Structure
 ### AbiU
+##### Example 1

 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /abiu/AbiU__AbiU-plddts_84.61928.pdb
+dataUrls:
+   - /abiu/AbiU__AbiU.cif
+
 ---
 ::

 ## Experimental validation
+
 <mermaid>
 graph LR;
    Chopin_2005[<a href='https://doi.org/10.1016/j.mib.2005.06.006'>Chopin et al., 2005</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>
+
No results found