Re: [phenixbb] Does phenix have any utility to do the 2mFo-DFc composite omit map calculations?

Hi Donnie, Thanks for the note; I'll check into it. The SGE mechanism is very simple and perhaps it will be applicable to other queueing systems without modification. For example if you queue jobs with: queue_command_here -flags -etcetc myjob.sh then you just give the GUI/autobuild/ligandfit the command run_command="queue_command_here -flags -etcetc" and then it runs the jobs as above. All the best, Tom T On Nov 3, 2010, at 8:21 AM, Donnie Berkholz wrote:

On 18:12 Tue 02 Nov , Nathaniel Echols wrote:

...

On Tue, Nov 2, 2010 at 6:02 PM, wrote:

...

I tried a dimer of 4000aa at 3.2A using the following script:

phenix.autobuild data=2VZ8.mtz model=${f}.pdb composite_omit_type=simple_omit

It took hours and ended up with nothing (probably due to memory leaking). Is there anyway to make it faster?

This is what the 'nproc' argument does - you should use as many processors as you have available. If you can distribute it across a queuing system, even better. (The GUI can set this up for you semi-automatically if you have Sun Grid Engine, but it's possible on the command line too - check the documentation for details.)

Now that new versions of SGE will no longer be free thanks to Oracle's purchase, have you considered adding support for a queueing system that is free and open-source, such as Torque?

-- Thanks, Donnie

Donald S. Berkholz, Ph.D. Research Fellow James R. Thompson lab, Physiology & Biomedical Engineering Grazia Isaya lab, Pediatric & Adolescent Medicine Medical Sciences 2-66 Mayo Clinic College of Medicine 200 First Street SW Rochester, MN 55905 office: 507-538-6924 cell: 612-991-1321 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss