[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.


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

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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