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