[phenixbb] phenix.find_ncs

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Jan 11 10:16:04 PST 2012

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 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
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb

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