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

Eric Pettersen pett at cgl.ucsf.edu
Sun Nov 25 17:32:53 PST 2007

On Nov 23, 2007, at 12:56 PM, Francesco Pietra wrote:
> Here I really don't understand. With your "including recent  
> changes" above, I
> understand that you follow 3.0 or 3.1 PDB format. Unless you add  
> that 3.0 and
> 3.1 formats are exercises not to follow (the official pdb booklet I  
> have, is V.
> 2.3, added of V. 3.0 and V 3.1). If you follow 3.0, modification of  
> Amber's
> file

As Elaine mentioned, v2.3 PDB files would place 'H' in column 14, so  
a 4-letter hydrogen name would be something like 1HD1, whereas in  
v3.0 they decided to just have the H start the name, producing names  
like HD11.  The fact that Chimera still produces v2.3 hydrogen names  
is wrong, and I have added your name to the bug-database entry for  
producing 3.0 names, but nonetheless the PDB changeover to 3.0 only  
happened a few months back, so most programs should be able to handle  
both forms.

> Finally, everything in the "classic" are is in view of MD. Even  
> DOCK is
> recommended as a preliminary to MD (by both Scott Brozell and D case).
> Therefore, it is a pity - to say politely - having to spend so much  
> effort in
> rectifying files from pre-programs. Unless Chimera is bound to some  
> other MD
> suite than Amber, to which MD suite Chimera's files flow in without  
> barriers.

Chimera isn't "bound" to any MD suite in particular.  It simply tries  
to produce standard PDB files.  The only software we've made a  
conscious attempt to coordinate with is DOCK.


	Eric Pettersen
	UCSF Computer Graphics Lab

More information about the Chimera-users mailing list