Bugs item #2117005, was opened at 2008-09-17 18:31
Message generated for change (Comment added) made by hansonr
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Category: Scripting
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Wayne Townsend-Merino (townsendmerino)
Assigned to: Bob Hanson (hansonr)
Summary: Trying to show ribbons doesn't work for biological molecules
Initial Comment:
Script doesn't work for biological molecule files, most of the time - for
example it doesn't work for 1PNR.
<script type="text/javascript">
jmolInitialize("/pdb/Viewers/jmol-11.6.RC14");
jmolCheckBrowser("popup", "../../browsercheck", "onClick");
jmolApplet(600, 'load "<%=pdbFile%>" FILTER "BIOMOLECULE <%=bioNum%>"');
jmolScriptWait("select all;spacefill off; wireframe off;cartoon;color cartoon
chain;");
jmolScriptWait("select ligand;wireframe 40;spacefill 120;");
</script>
Note the use of "FILTER BIOMOLECULE".
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>Comment By: Bob Hanson (hansonr)
Date: 2008-09-20 10:56
Message:
no follow-up on this? I'd like to get this cleared up if it's a real
problem.
Be aware that there are certain models -- for example, viral coats -- for
which an automated system such as this will surely fail. Jmol can report
the number of atoms that would be involved in a biomolecule, but it does
not hesitate to try to construct one that would fill memory completely. In
those cases you need to add the *.CA filter option.
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Comment By: Bob Hanson (hansonr)
Date: 2008-09-19 06:53
Message:
Thought I responded to this... guess not.
I cannot reproduce this problem. You sure it's not in your PHP code?
Certainly with 1PNR I see two Biomolecules, and they load perfectly using
load =1prn FILTER "BIOMOLECULE 1"
or
load =1prn FILTER "BIOMOLECULE 2"
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