[Molvis-list] rasmol connect bug

[Herbert J. Bernstein]

The sourceforge release announcement was on an earlier molvis
list message on 11 April 2008.  The URL is

   http://www.sourceforge.net/projects/openrasmol

=====================================================
  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
=====================================================

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 
> 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
>>
>> _______________________________________________
>> Molvis-list mailing list
>> Molvis-list at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/molvis-list
>
>
> -- 
> =====================================================
>   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
> =====================================================
>
> _______________________________________________
> Molvis-list mailing list
> Molvis-list at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/molvis-list

-- 
✐Richard Cook
✇ Lawrence Livermore National Laboratory
Bldg-453 Rm-4037, Mail Stop L-557
7000 East Avenue,  Livermore, CA, 94550, USA
☎ (office) (925) 423-9605
☎ (fax) (925) 423-6961
---
Information Management & Graphics Grp., Services & Development Div., 
Integrated Computing & Communications Dept.
(opinions expressed herein are mine and not those of LLNL)



_______________________________________________
Molvis-list mailing list
Molvis-list at bioinformatics.org
http://www.bioinformatics.org/mailman/listinfo/molvis-list