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

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