Hi Ursula, Thanks for sending me the file...you can find all 3 groups this way: phenix.simple_ncs_from_pdb your_pdb.pdb \ maximize_size_of_groups=true Here the parameter maximize_size_of_groups is available in simple_ncs_from pdb (but not from find_ncs): maximize_size_of_groups= False You can request that the scoring be set up to maximize the number of members in NCS groups In your case the chains in your file are not all quite the same, so the ncs-finding algorithm took the group that gave the longest match (and skipped one chain). Setting maximize_size_of_groups=true will change the scoring to try and keep as many members as possible. I think that I will make this the default... All the best, Tom T
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.
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220