[phenixbb] ncs resolve

[Thomas C. Terwilliger]

Hi Georg,

I think that if phenix.find_ncs says

No NCS found...you might try ncs_in_type=sites

then it is interpreting the sites as parts of chains and is trying to find
NCS in those chains, while what you want is for it to interpret these as
sites and to find ncs in the sites.  So I wonder if you did try adding the
keyword ncs_in_type as in:

phenix.find_ncs my_sites.pdb my_map_coeffs.mtz ncs_in_type=sites

If that failed, then I would suggest trying fewer sites that are more
separated: perhaps 3 or 4 sites per monomer, as far apart as possible.

If that fails (or maybe as your first try actually), take the entire
helix, and make 2 copies A and B, placing them in their appropriate
places, and then feed these to phenix with:

phenix.simple_ncs_from_pdb my_two_copies.pdb

and that may do it for you.

All the best,
Tom T


>> Dear phenix users,
>>
>> luckily autobuild could solve my SAD problem, but didn´t find any NCS.
>> Although the protein is a dimer. I analysed the structure in coot now and
>> SSM superposed a homolog protein (just one chain) which (fits quite good)
>> on
>> chain A and B. I then could find a helix which was built in chain A and B,
>> I
>> took the 8 corresponding aminoacids from A and B and run:  phenix.find_ncs
>> overall_best_denmod_map_coeffs.mtz overall_best198206ca155163b.pdb with
>> and
>> without ncs_parameters.force_ncs=True and didn´t get any solution.
>>
>> The program gives me an output saying: No NCS found...you might try
>> ncs_in_type=sites
>>
>> Any suggestions whats wrong and a smarter way to do this.
>>
>> Thanks in advance Georg.
>>
>> -----Ursprüngliche Nachricht-----
>> Von: phenixbb-bounces at phenix-online.org
>> [mailto:phenixbb-bounces at phenix-online.org] Im Auftrag von Thomas Stout
>> Gesendet: Freitag, 18. Dezember 2009 23:56
>> An: PHENIX user mailing list
>> Betreff: Re: [phenixbb] queueing systems
>>
>>
>>
>> We don't use PHENIX, but we do use several queueing systems on three
>> different clusters.
>>
>> SGE is bulletproof and highly recommended.
>>
>> Condor has some degree of "evilness" -- especially under Windows.  I have
>> found it prone to grabbing resources indiscriminately and also being very,
>> very resistant to uninstallation.  Your mileage may vary.
>>
>> Certain implementations of "torque" are broken - stay away, or at least be
>> very cautious and enter with your eyes open.
>>
>> Cheers,
>> Tom
>>
>>
>> -----Original Message-----
>> From: phenixbb-bounces at phenix-online.org on behalf of Phil Evans
>> Sent: Fri 12/18/2009 2:47 PM
>> To: PHENIX user mailing list
>> Subject: Re: [phenixbb] queueing systems
>>
>>
>> Dear Nat
>>
>> We use Sun grid engine
>>
>> Phil
>>
>> On 18 Dec 2009, at 18:47, Nathaniel Echols wrote:
>>
>>> Hi all--
>>>
>>> I'd like to hear what kinds of queueing systems people are using for
>>> running Phenix on managed clusters.  The eventual goal - if feasible -
>>> is to add support for submitting jobs directly from the Phenix GUI.
>>> Anyone who is interested, please send me (not the list) a brief email
>>> describing a) the OS, b) the queueing software, and c) the submission
>>> method (i.e. shell script, configuration file, simple command).
>>> (Also, anyone who is willing to help test this if and when it becomes
>>> available, let me know - I have access to Sun Grid Engine and Condor
>>> already, but it's probably going to be difficult to test anything else
>>> personally.)
>>>
>>> thanks,
>>> Nat
>>>
>>> --------------------
>>> Nathaniel Echols
>>> Lawrence Berkeley Lab
>>> 510-486-5136
>>> NEchols at lbl.gov
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
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