Re: [ccp4bb]: Refining occ's of alternate configs: Which program?

[Frank von Delft <frank@cryst.bioc.cam.ac.uk>]

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> I'm trying to refine alternate configurations of substrates
> in an active site.  This was once possible in x-plor, so I'm
> using CNS.  But the cns-bug-reporter told me that they haven't 
> yet implimented the option to refine alternate configuration 
> occupancies in CNS.  As you can imagine, since it's my active 
> site, my chemical arguement sorta relys on it.  So, I need to
> find a program that will do it.

Hi Diane, CNS does do it, it's all a matter of what the pdb file looks 
like.  Have a look at Gerard Kleywegt's ACONIO to get you from O to CNS
formats, and also the alternate.inp script of CNS (top of the page).

> I looked at the documentation for refmac, but don't see
> anything obvious in the docs or the examples that flags 
> to refine occ's of alternate configurations.

I don't think refmac refines occupancies (yet).  But you can certainly
have alterative conformations, just set occupancies to 0.5 and add the A
or B card in the column before the residue name, which is default pdb
format:

ATOM     16  SD AMET    16      90.640  79.154  32.608  0.50 51.85
ATOM     16  SD BMET    16      90.640  81.154  33.608  0.50 51.85  
               ^^^                                      ^^^^

(As far as I remember) protin is then quite happy with it and as
long as occupancies are not 1 refmac doesn't care about collisions. 
(Correct me if I'm wrong).

Good luck
Phraenquex