[Molvis-list] rasmol connect bug
Herbert J. Bernstein
yaya at bernstein-plus-sons.com
Thu Apr 17 21:47:07 EDT 2008
The sourceforge release announcement was on an earlier molvis
list message on 11 April 2008. The URL is
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
yaya at dowling.edu
On Thu, 17 Apr 2008, Rich Cook wrote:
> I didn't even know there was a sourceforge page -- suggest you put
sourceforge URL into the list signature.
On Apr 16, 2008, at 7:27 PM, Herbert J. Bernstein wrote:
> Thank you for the problem report. Until we locate the bug, you can
> bonding one atom pair at a time with the bond command, e.g.
> bond 0 1
> bond 0 2
> bond 1 2
> I have entered the report into the tracker on sourceforge for you.
> H. J. Bernstein
> At 7:04 PM -0500 4/16/08, Michael Sternberg wrote:
>> Dear Rasmol users,
>> I'm encountering a bug in the "connect" command, wherein certain
>> bonds are not detected, come what may.
>> Consider the following xyz-file, which is an excerpt from a larger
>> model of a surface I'm trying to render:
>> ==== test.xyz ================================
>> Ni 2.74059 4.93685 0.02301
>> Ni 1.31849 7.41686 0.03767
>> Ni 4.16141 7.41082 0.01675
>> These 3 atoms are arranged in a roughly equilateral triangle with
>> distances 2.843, 2.853 and 2.859 Angstroms.
>> Run any rasmol version 2.6.4 to the very latest
>> rasmol -xyz test.xyz
>> RasMol> connect on
>> This will draw just *one* bond, not three. Curiously, it's the
>> *middle* length bond that's detected, not the shorter or longer ones.
>> This shortcoming of rasmol's bond detection has bugged me on and off
>> for quite some time. Usually, I got around it by re-declaring the
>> offending atoms to be types with larger covalent radii. That won't
>> work in the full structure that I'm handling here, as it introduces
>> unphysical bonds in other parts of the structure. I may have some
>> recourse in supplying bond info trough, say, the alchemy format, but
>> I wonder if the root of this isn't a shortcut taken in the bond
>> detection routine?
>> Regards, Michael
>> Molvis-list mailing list
>> Molvis-list at bioinformatics.org
> Herbert J. Bernstein, Professor of Computer Science
> Dowling College, Kramer Science Center, KSC 121
> Idle Hour Blvd, Oakdale, NY, 11769
> yaya at dowling.edu
> Molvis-list mailing list
> Molvis-list at bioinformatics.org
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