[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 ================================

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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