[Chimera-users] Fwd: carbon-chlorine bond

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 18 09:19:12 PST 2008


Hi Francesco,
I believe that correct PDB format includes atom names with the element  
symbol right-justified in 13-14.  So if the element symbol is one  
character (C,N,O,H,...) it should appear in column 14.  If the element  
is two characters (CL,CA,FE,...) it should appear in columns 13-14.   
The exception to this rule is if a hydrogen name has four characters,  
it begins at 13.

This is the pattern observed in the current (remediated) PDB files  
from RCSB and other wwPDB sites.
<http://remediation.wwpdb.org/documentation/format32/sect9.html#ATOM>
<http://remediation.wwpdb.org/documentation/format32/sect9.html#HETATM>

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#errors 
 >

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html



On Nov 18, 2008, at 12:18 AM, Francesco Pietra wrote:

> Elaine:
> In the fear that docking and MD had been carried out with C in place
> of Cl for the ligand, I checked all. OK, correct for Cl.
>
> I noticed that when all atom names are left-justifies in column 13,
> Chimera reports the structures correctly.When all atom names are
> left-justified in column 14, Chimera does not report Cl correctly.
>
> I  writing pdb files, the various programs in DOCK/Amber are not well
> consistent (although I did not carry out a thorough search). Dock6
> writes the final pose pdb for receptor+ligand by left-justifying all
> atom names in column 13. Amber behaves differently according to which
> internal program is used.
>
> francesco
>




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