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 < [email protected]> 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 [email protected] 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