[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

> 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

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