[Chimera-users] Chimera vs Amber, which one digresses from the average pdb rules?
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
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
> 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
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.
UCSF Computer Graphics Lab
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