[Molvis-list] "New" Chime bug: MODELS vs. CONECT records

Eric Martz emartz at microbio.umass.edu
Fri Apr 15 13:38:45 EDT 2005

Dear Inbal,

Your observations, plus more of my own, show that we have discovered a bug 
in Chime that I did not know about: It appears (see below) that when 
MODEL/ENDMDL records are used, Chime fails to obey CONECT records.

I have not come up with a solution in Chime. I am quite sure that MDL will 
not fix this bug even if we ask them.

But this is why many people, especially Miguel Howard, have spent so much 
time on jmol! (www.jmol.org) jmol should be able to do exactly what you 
want -- and if not (or if there are bugs) someone (probably Miguel) will 
fix them! (In addition, it will work on linux and native OSX/Safari as well 
as all Chime-compatible browsers.) So I think if you switch to jmol, you 
can acheive your goals.

Chime also supports XYZ format for multiple models, and (unlike NMR-PDB 
format, has built-in support for animation). XYZ format is appropriate for 
small/inorganic molecules but not for proteins or nucleic acids (because it 
has no way to specify the position of an element in a group (e.g. CA = 
Carbon Alpha in PDB format) nor the group to which an atom belongs (so no 
amino acids nor nucleotides). I have no experience with XYZ format so I 
cannot tell you if you can get the bond display you want in Chime with XYZ.

Here are my observations in Chime:

Your model of sulfur hexafluoride specifies six S-F bonds but no F-F bonds. 
By default, with your two model file, Chime shows the unwanted F-F bonds.

When a single model is extracted from your 2-model PDB file (WITHOUT 
Chime behaves correctly. By default, it shows only the S-F bonds. This is 
because, when the number of bonds specified in CONECT records is equal to 
or greater than (number of ATOMs + number of HETATMs - number of chains), 
Chime goes automatically into "set connect false" mode, showing only the 
bonds specified by CONECT records, not the bonds Chime normally calculates 
for proteins based on interatomic distances. This is all documented at

(Removing a single CONECT record correctly makes Chime default to showing 
the F-F bonds; entering "set connect false" before loading correctly makes 
Chime show only the 5 remaining S-F bonds.)

However, when the single model is enclosed between MODEL 1/ENDMDL records 
(still only one model present) Chime shows the unwanted F-F bonds (so is 
failing to go into "set connect false" mode). Further, if you issue an 
explicit "set connect false" command before loading the model, NO bonds are 
shown. This is a second bug -- failure to process CONECT records when even 
a single MODEL record is present. The same behavior is seen with your 
original 2-model PDB file.

The only possible workaround I thought of was to load the model with "load 
nmrpdb filename.pdb" but that failed to correct either problem.

Sincerely, -Eric

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