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.<br><br>Ursula<br><br><div class="gmail_quote">On Wed, Jan 11, 2012 at 10:16 AM, Thomas C. Terwilliger <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Ursula,<br>
<br>
I am not sure why find_ncs did not get the 3rd chain for the third group.<br>
I think that when you run phenix.refine it is (for the moment) actually<br>
just calling find_ncs to get the NCS groups, so the groups found there<br>
should (if everything is working the way I think it should) be identical<br>
to the ones you would find with phenix.find_ncs.<br>
<br>
Here is something to try: Split your model into just protein #3 (you can<br>
use phenix.pdbtools and keep="chain C or chain F or chain I" to do this),<br>
and also just protein #1 and #2. �Then run find_ncs separately on these.<br>
Can find_ncs get the ncs for your 3 copies of protein #3 all by<br>
themselves?<br>
<br>
If not...then it indicates that perhaps one of the chains is actually<br>
different (maybe very different conformation, maybe mostly missing, maybe<br>
different sequence...?)<br>
<br>
All the best,<br>
Tom T<br>
<div><div class="h5"><br>
<br>
�>> I am working with a complex of 3 different proteins, and there are 3<br>
>> complexes in the asymmetric unit. During phenix.refine I used automatic<br>
>> NCS<br>
>> and it worked fine. I now wanted to determine the NCS parameters with<br>
>> phenix.find_ncs. The output file gives me 3 NCS groups, 2 groups with 3<br>
>> chains, and 1 group with 2 chains.I cannot figure out why one chain is not<br>
>> included. I tried to run it with only pdb input, or pdb anf map<br>
>> coefficients, same result. Any suggestions hat else to try?<br>
>><br>
>> Thanks<br>
>><br>
>> Ursula<br>
>><br>
>> --<br>
>> Ursula Schulze-Gahmen, Ph.D.<br>
>> Assistant Researcher<br>
>> UC Berkeley, QB3<br>
>> 356 Stanley Hall #3220<br>
>> Berkeley, CA 94720-3220<br>
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<br>
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</blockquote></div><br><br clear="all"><br>-- <br>Ursula Schulze-Gahmen, Ph.D.<br>Assistant Researcher<br>UC Berkeley, QB3<br>356 Stanley Hall #3220<br>Berkeley, CA 94720-3220<br><br>