Bugs item #3501723, was opened at 2012-03-11 04:24 Message generated for change (Comment added) made by aherraez You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3501723&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Applet Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Robert Davis (elrobo) Assigned to: Bob Hanson (hansonr) Summary: Possible bug with link cards Initial Comment: This pdb file gives an "unrecognized file format" error: http://dev.glycam.org/userdata/tools/mdfiles/ecd0d1df-bdb8-4add-939f-5180b547a705/2.pdb. The error also includes the first three lines of the pdb file (link cards). When I remove the third link card, it works. Here's the file: http://dev.glycam.org/userdata/tools/mdfiles/ecd0d1df-bdb8-4add-939f-5180b547a705/1.pdb. I am invoking jmol like this: jmolApplet([200, 400], "load /userdata/tools/mdfiles/ecd0d1df-bdb8-4add-939f-5180b547a705/2.pdb"); ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2012-03-11 04:50 Message: Another solution is to insert a first line with either "HEADER " or "REMARK " Also note that Jmol will ignore the LINK lines, so you probably may remove them without any effects, and that makes Jmol understand them as pdb format since it will read the HETATM key But my first solution is the safest, just tell it it is pdb with the pdb:: prefix. ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2012-03-11 04:46 Message: Hi Robert. This is not a bug. Your pdb file is nonstandard and hence Jmol needs some hints to know this is a pdb-formatted file. I guess the difference you see between files 1 and 2 is purely random. So try to instruct Jmol to read it as a pdb file: jmolApplet([200, 400], "load pdb::/userdata/tools/mdfiles/ecd0d1df-bdb8-4add-939f-5180b547a705/2.pdb"); See "load" in the scripting documentation for more details ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3501723&group_id=23629 ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
