[Chimera-users] Chimera vs Amber, which one digresses from the average pdb rules?

[Elaine Meng]

Hi Francesco,
In Chimera we have worked to create PDB files in the correct format,  
as described at the PDB web site:
http://www.wwpdb.org/docs.html

We also have a brief intro to this format in the Chimera documentation:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
framepdbintro.html

We decided the best approach would be to follow the format standard,  
including recent changes. However, lots of other programs don't  
follow the standard, and when using multiple programs it is usually  
necessary to hand-edit or use scripts to convert files.

In version 2.3 PDB format, the atom name occupies columns 13-16 with  
the element symbol right-justified in 13-14.  So if the element  
symbol is one character, it is supposed to be in column 14, not 13, i.e.
C315 should be 5C31.  The output you are getting follows this role.

In version 3.0 PDB format, that is still true, except for hydrogen  
atoms.

Both versions follow the HETATM/ATOM rules I mentioned earlier.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html