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SandboxC

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(New page: {{StructureC |PDB= {{{PDB}}}|SCENE={{{SCENE}}}|SIZE={{{SIZE|350}}}|CAPTION={{{CAPTION|2hhd, resolution 2.20&Aring; (<scene name='initialview01'>initial scene</scene>)}}} |LIGAND= <scene na...)
Current revision (20:18, 13 August 2008) (edit) (undo)
 
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{{StructureC
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{{STRUCTURE_2hhdC | PDB=2hhd | SCENE= }}
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|PDB= {{{PDB}}}|SCENE={{{SCENE}}}|SIZE={{{SIZE|350}}}|CAPTION={{{CAPTION|2hhd, resolution 2.20&Aring; (<scene name='initialview01'>initial scene</scene>)}}}
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|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01040 globin]</span>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2hhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hhd OCA], [http://www.ebi.ac.uk/pdbsum/2hhd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2hhd RCSB]</span>
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|FUNCTION={{GO|id=GO:0019825 | text = oxygen binding}}{{GO|id=GO:0005515 | text = protein binding}}{{GO|id=GO:0046872 | text = metal ion binding}}{{GO|id=GO:0005344 | text = oxygen transporter activity}}{{GO|id=GO:0020037 | text = heme binding}}{{GO|id=GO:0005506 | text = iron ion binding}}{{GO|id=GO:0030492 | text = hemoglobin binding}}{{GO|id=GO:0008430 | text = selenium binding}}
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|PROCESS={{GO|id=GO:0006810 | text = transport}}{{GO|id=GO:0015671 | text = oxygen transport}}{{GO|id=GO:0045429 | text = positive regulation of nitric oxide biosynthetic process}}{{GO|id=GO:0030185 | text = nitric oxide transport}}{{GO|id=GO:0050880 | text = regulation of blood vessel size}}{{GO|id=GO:0008217 | text = regulation of blood pressure}}
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|COMPONENT={{GO|id=GO:0005833 | text = hemoglobin complex}}
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|SARESOURCES=<span class='plainlinks'>CATH : [http://www.cathdb.info/cgi-bin/cath/Domain.pl?domain_id=2hhdA00 2Hhda00], [http://www.cathdb.info/cgi-bin/cath/Domain.pl?domain_id=2hhdB00 2Hhdb00], [http://www.cathdb.info/cgi-bin/cath/Domain.pl?domain_id=2hhdC00 2Hhdc00], [http://www.cathdb.info/cgi-bin/cath/Domain.pl?domain_id=2hhdD00 2Hhdd00]<br>InterPro : [http://www.ebi.ac.uk/interpro/ISearch?query=IPR002339 Ipr002339], [http://www.ebi.ac.uk/interpro/ISearch?query=IPR002338 Ipr002338], [http://www.ebi.ac.uk/interpro/ISearch?query=IPR000971 Ipr000971], [http://www.ebi.ac.uk/interpro/ISearch?query=IPR009050 Ipr009050], [http://www.ebi.ac.uk/interpro/ISearch?query=IPR002337 Ipr002337], [http://www.ebi.ac.uk/interpro/ISearch?query=IPR012292 Ipr012292]<br>Pfam : [http://pfam.sanger.ac.uk/family?acc=PF00042 PF00042]<br>SCOP : [http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?search_type=SCOP&amp;key=15312 d2hhda_], [http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?search_type=SCOP&amp;key=15489 d2hhdb_], [http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?search_type=SCOP&amp;key=15313 d2hhdc_], [http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?search_type=SCOP&amp;key=15490 d2hhdd_]<br>UniProt : [http://ca.expasy.org/cgi-bin/niceprot.pl?P69905 P69905], [http://ca.expasy.org/cgi-bin/niceprot.pl?P68871 P68871]</span>
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|FARESOURCES=<span class='plainlinks'>GeneCard : [http://www.genecards.org/cgi-bin/carddisp.pl?id=HBA1, HBA1,]</span>
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|CONSURFLOCALANALYSIS={{!}}-
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{{!}} colspan="2" style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;" {{!}} [[Image:Consurf_key_small.gif|center]]
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{{!}}-{{!}} style="background-color:#bac9f7;color:#040d44;vertical-align:top;text-align:left;"
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{{!}} '''Toggle Conservation Colors:'''
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{{!}} align="left" style="background-color:#acfaac;border-top:2px solid #dddddd; border-right:2px solid #dddddd" {{!}}
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Rows = identical sequences:
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<jmol>
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It works! Just need to set the buttons checked on start.
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<jmolButton>
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<script>if (consurf_A!=0); select:A; spacefill off;color translucent -1;
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consurf_A= 0;javascript "document.getElementById('jmb_A').value='A [ ]'";
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else; select:A; spacefill on; color opaque;consurf_A = 1;javascript
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"document.getElementById('jmb_A').value='A [x]';"; endif;</script>
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<text>A [ ]</text>
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<name>jmb_A</name>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script>if (consurf_C!=0); select:C; spacefill off;color translucent -1;
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consurf_C= 0;javascript "document.getElementById('jmb_C').value='C [ ]'";
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else; select:C; spacefill on; color opaque;consurf_C = 1;javascript
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"document.getElementById('jmb_C').value='C [x]';"; endif;</script>
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<text>C [ ]</text>
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<name>jmb_C</name>
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</jmolButton>
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</jmol>
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<jmol>
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----
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<jmolButton>
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[[User:Eric Martz|Eric Martz]] 22:47, 13 August 2008 (IDT): Agreed, it looks great (after the buttons are checked at start) and it already WORKS CORRECTLY!
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<script>if (consurf_B!=0); select:B; spacefill off;color translucent -1;
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consurf_B= 0;javascript "document.getElementById('jmb_B').value='B [ ]'";
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else; select:B; spacefill on; color opaque;consurf_B = 1;javascript
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"document.getElementById('jmb_B').value='B [x]';"; endif;</script>
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<text>B [ ]</text>
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<name>jmb_B</name>
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</jmolButton>
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</jmol>
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<jmol>
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<jmolButton>
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<script>if (consurf_D!=0); select:D; spacefill off;color translucent -1;
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consurf_D= 0;javascript "document.getElementById('jmb_D').value='D [ ]'";
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else; select:D; spacefill on; color opaque;consurf_D = 1;javascript
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"document.getElementById('jmb_D').value='D [x]';"; endif;</script>
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<text>D [ ]</text>
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<name>jmb_D</name>
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</jmolButton>
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</jmol>
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{{!}}-
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I added a link ''Caveat'' which will go to a section (to be written) in [[Conservation, Evolutionary]] that explains that the conservation level colors in sequence-different chains don't have the same quantitative meaning (explained better than this).
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}}
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Also needed: under Further Information, the link "Complete Results at ConSurfDB" needs to go to the correct PDB code at ConSurfDB. Before we can do that, I need to know:
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# How to specify the PDB code in a consurfdb url.
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# How to insert the variable PDB code into the URL for the "Complete Results" link in the Template:StructureC

Current revision

PDB ID 2hhd

Drag the structure with the mouse to rotate

It works! Just need to set the buttons checked on start.

Eric Martz 22:47, 13 August 2008 (IDT): Agreed, it looks great (after the buttons are checked at start) and it already WORKS CORRECTLY!

I added a link Caveat which will go to a section (to be written) in Conservation, Evolutionary that explains that the conservation level colors in sequence-different chains don't have the same quantitative meaning (explained better than this).

Also needed: under Further Information, the link "Complete Results at ConSurfDB" needs to go to the correct PDB code at ConSurfDB. Before we can do that, I need to know:

  1. How to specify the PDB code in a consurfdb url.
  2. How to insert the variable PDB code into the URL for the "Complete Results" link in the Template:StructureC
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