[phenixbb] phenix.find_ncs

Thomas C. Terwilliger terwilliger at lanl.gov
Wed Jan 11 16:23:48 PST 2012


Hi Ursula,

In that case...sounds like something I need to fix!  Would it be possible
to send me (off-list, terwilliger at lanl.gov) the entire PDB file and I'll
have a look?

In the meantime, I guess if you run each group separately you have the
information that you are looking for...

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 <
>> 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
>>> >> phenixbb at phenix-online.org
>>> >> 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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