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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: [email protected] [mailto:[email protected]] 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: [email protected] 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 [email protected]
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