[Molvis-list] rasmol connect bug

Michael Sternberg sternberg at anl.gov
Sun Apr 20 13:16:45 EDT 2008


Hi,

Thanks Herbert.  I located the "not-really" bug - it is due to  
optimization and rather simple to fix:

In molecule.c, change
	#define AbsMaxBondDist 600
to
	#define AbsMaxBondDist 800

Roger implemented fast progressive short-circuit evaluation of  dx^2 +  
dy^2 + dz^2 > AbsMaxBondDist^2, and 600 (=2.4 A) was just a tad too  
short for metal bonds that are aligned to the axes; 800 (3.2 Angstrom)  
works fine now, but could possibly be even 1000.

The performance impact of a larger value is negligible on today's  
machines ;-)


Regards, Michael

On Apr 16, 2008, at 21:27 , Herbert J. Bernstein wrote:
> 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.
>
> Regards,
>  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
>>
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>
>
> -- 
> =====================================================
> Herbert J. Bernstein, Professor of Computer Science
>   Dowling College, Kramer Science Center, KSC 121
>        Idle Hour Blvd, Oakdale, NY, 11769
>
>                 +1-631-244-3035
>                 yaya at dowling.edu
> =====================================================




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