[Molvis-list] rasmol connect bug
Michael Sternberg
sternberg at anl.gov
Wed Apr 16 20:04:22 EDT 2008
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
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