[Molvis-list] rasmol connect bug

Herbert J. Bernstein yaya at bernstein-plus-sons.com
Wed Apr 16 22:27:05 EDT 2008

Thank you for the problem report.  Until we locate the bug, you can force
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 ================================
>    3
>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_2_7_4_2_10Apr08:
>      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

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