Does phenix have any utility to do the 2mFo-DFc composite omit map calculations? - phenixbb - phenix-online.org

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

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zhangh1＠umbc.edu

2 Nov 2010 2 Nov '10

6 p.m.

Hi, Does phenix have any utility to do the 2mFo-DFc composite omit map calculations (similar to OMIT in CCP4)? Thanks in advance! Hailiang

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Tom Terwilliger

2 Nov 2 Nov

6:06 p.m.

New subject: Does phenix have any utility to do the 2mFo-DFc composite omit map calculations?

Hi Hailiang, Yes, you can do this with autobuild: phenix.autobuild data=data.mtz model=coords.pdb composite_omit_type=simple_omit nproc=4 (or nproc=however many processors you have) It's pretty quick. All the best, Tom T On Nov 2, 2010, at 12:00 PM, [email protected] wrote:

Hi,

Does phenix have any utility to do the 2mFo-DFc composite omit map calculations (similar to OMIT in CCP4)? Thanks in advance!

Hailiang

_______________________________________________ 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

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zhangh1＠umbc.edu

3 Nov 3 Nov

1:02 a.m.

Hi Tom: 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? Thanks! Hailiang

Hi Hailiang, Yes, you can do this with autobuild:

phenix.autobuild data=data.mtz model=coords.pdb composite_omit_type=simple_omit nproc=4 (or nproc=however many processors you have)

It's pretty quick.

All the best, Tom T On Nov 2, 2010, at 12:00 PM, [email protected] wrote:

...
Hi,

Does phenix have any utility to do the 2mFo-DFc composite omit map calculations (similar to OMIT in CCP4)? Thanks in advance!

Hailiang

_______________________________________________ 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Nathaniel Echols

1:12 a.m.

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.) Unlike the CCP4 OMIT program, it is actually re-refining many partial models to remove phase bias, so running it on a single processor isn't going to work very well. -Nat

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zhangh1＠umbc.edu

3:09 a.m.

Got it! Thanks!

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.) Unlike the CCP4 OMIT program, it is actually re-refining many partial models to remove phase bias, so running it on a single processor isn't going to work very well.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Donnie Berkholz

2:21 p.m.

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

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Nathaniel Echols

2:44 p.m.

On Wed, Nov 3, 2010 at 7:21 AM, Donnie Berkholz wrote:

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?

I didn't realize that Oracle was going to start charging for SGE - not too surprising though. As far as AutoBuild on the command line is concerned, you can use any queuing system you want, it's just more work to set up (and not really supported). For the GUI, I'm happy to support other platforms but this would require actually setting them up and testing them, and we're stretched pretty thin here already. If you have something set up already and are willing to give me an account, that would be sufficient motivation for me to spend some time on it. I think one of the pharma companies managed to get it working on a commercial product called LSF, but they aren't going to give me access to their computers, obviously. I have an account on systems running Condor, which is free (and probably Free), but their current setup is broken in such a way that makes it difficult to support. I may be able to talk the sysadmins into fixing this; stay tuned. I'm not sure what other systems are in widespread use, but I'm more inclined to spend time on those that are free (at least to academics). When I asked about this a year or so ago, everyone who responded asked for SGE (plus one for Apple's Xgrid, which is quite a bit more work). -Nat

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Tom Terwilliger

5:06 p.m.

New subject: 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

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Donnie Berkholz
Nathaniel Echols
Tom Terwilliger
zhangh1＠umbc.edu