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

Tom Terwilliger terwilliger at lanl.gov
Wed Nov 3 10:06:02 PDT 2010

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,  <zhangh1 at umbc.edu> 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
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

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