[phenixbb] phenix.find_ncs

Ursula Schulze-Gahmen uschulze-gahmen at lbl.gov
Wed Jan 11 10:46:15 PST 2012


Does the sequence have to be identical? It could be that I mutated some
residues to alanine.

Ursula

On Wed, Jan 11, 2012 at 10:16 AM, Thomas C. Terwilliger <
terwilliger at lanl.gov> wrote:

> Hi Ursula,
>
> I am not sure why find_ncs did not get the 3rd chain for the third group.
> I think that when you run phenix.refine it is (for the moment) actually
> just calling find_ncs to get the NCS groups, so the groups found there
> should (if everything is working the way I think it should) be identical
> to the ones you would find with phenix.find_ncs.
>
> Here is something to try: Split your model into just protein #3 (you can
> use phenix.pdbtools and keep="chain C or chain F or chain I" to do this),
> and also just protein #1 and #2.  Then run find_ncs separately on these.
> Can find_ncs get the ncs for your 3 copies of protein #3 all by
> themselves?
>
> If not...then it indicates that perhaps one of the chains is actually
> different (maybe very different conformation, maybe mostly missing, maybe
> different sequence...?)
>
> All the best,
> Tom T
>
>
>  >> I am working with a complex of 3 different proteins, and there are 3
> >> complexes in the asymmetric unit. During phenix.refine I used automatic
> >> NCS
> >> and it worked fine. I now wanted to determine the NCS parameters with
> >> phenix.find_ncs. The output file gives me 3 NCS groups, 2 groups with 3
> >> chains, and 1 group with 2 chains.I cannot figure out why one chain is
> not
> >> included. I tried to run it with only pdb input, or pdb anf map
> >> coefficients, same result. Any suggestions hat else to try?
> >>
> >> Thanks
> >>
> >> Ursula
> >>
> >> --
> >> Ursula Schulze-Gahmen, Ph.D.
> >> Assistant Researcher
> >> UC Berkeley, QB3
> >> 356 Stanley Hall #3220
> >> Berkeley, CA 94720-3220
> >> _______________________________________________
> >> phenixbb mailing list
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> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >>
>
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-- 
Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220
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