[phenixbb] ncs resolve

Georg Mlynek georg.mlynek at univie.ac.at
Fri Dec 18 15:37:18 PST 2009

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

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. 


-----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


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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