Bugs item #2904986, was opened at 2009-11-27 08:03
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: Nobody/Anonymous (nobody)
Assigned to: Bob Hanson (hansonr)
Summary: error selecting an atom
Initial Comment:
environment:
mac osx ff3.5
Jmol 11.8.10
attached pdb file
select 296:A.CD;
gives an error:
select { 296 and *:A and *. <<<<
script compiler ERROR: invalid expression token: cd
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>Comment By: Bob Hanson (hansonr)
Date: 2009-11-27 19:50
Message:
fixed for 11.8.11; not a problem in 11.9.9
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Comment By: Angel Herraez (aherraez)
Date: 2009-11-27 08:58
Message:
I can confirm this on Jmol 11.8.4 in the PDB site (Ff 3.5, WinXP).
Of course this shouldn't happen. Either it is a conflict with cadmium, as
Miguel points out, or with the (relatively recent) "cd" command
http://chemapps.stolaf.edu/jmol/docs/#cd
Bob will surely be able to fix that.
Since the involved atom is the delta carbon in Lysine, many files will
suffer this bug!
As a work-around, I find that this works fine:
select 296:A.CD?;
Since
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Comment By: Miguel (migueljmol)
Date: 2009-11-27 08:32
Message:
It has been several years since I have worked on Jmol, so I am not the
right person to work on this. With that caveat ...
My initial thought is that the CD token is being interpreted as Cadmium,
and that the interpreter is croaking because of that. Of course, I may be
completely mistaken. I am going to reassign this to Bob.
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Comment By: Alexander Rose (morem)
Date: 2009-11-27 08:22
Message:
... and shows the same error, the attached file is somewhat cleaned
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Comment By: Alexander Rose (morem)
Date: 2009-11-27 08:20
Message:
the original pdb file is
http://www.rcsb.org/pdb/explore/explore.do?structureId=3DQB
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