uschulze-gahmen at lbl.gov
Wed Jan 11 10:52:27 PST 2012
I just did waht you suggested. I ran phenix.find_ncs on the problem group
only. This time it found all 3 chains in the group.
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
> 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
> >> 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
> >> _______________________________________________
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Ursula Schulze-Gahmen, Ph.D.
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220
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