#526 Possible bug with link cards

open
Applet (71)
5
2012-03-11
2012-03-11
No

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");

Discussion

  • Angel Herraez

    Angel Herraez - 2012-03-11

    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

     
  • Angel Herraez

    Angel Herraez - 2012-03-11

    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.

     
  • Robert Davis

    Robert Davis - 2012-03-11

    Thanks!

     
  • Bob Hanson

    Bob Hanson - 2012-03-11

    fixed for 12.2.18 and 12.3.18. Jmol wasn't looking for LINK records in the first 16 lines.

     

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