August 2006 - phenixbb - phenix-online.org

Re: [phenixbb] phase extension through phenix
by Tom Terwilliger 11 Aug '06

11 Aug '06

Hi Pramod, >I have one more question. Is any way in phenix GUI through which i can do >phasing to lowere resolution, further phase extension to higher >resolution? Becouse, my SAD data with single SeMet in whole protein of >3.5 Ang which have somewhat better phases and FOM at 5.0 ang resolution >than 3.5 Ang resolution. Is it possible through phenix? >If anybody have any one can help me? In the version you have, unfortunately the AutoSol keywords res_phase and resolution do almost the same thing, so you cannot do what you are asking for. This is fixed for the next version. An update patch will be available shortly to do it as well. I'm sorry for the problem! -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov 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.tbgenomics.org

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SAD and autosol
by Tom Terwilliger 11 Aug '06

11 Aug '06

Hi Pramod, >Hi all I am new user of the phenix. I am using autosol for the SAD data of >the 3.5 Ang of resolution data of spacegroup P42212. After running autosol >with all inputs , during Hyss autosol is not able to move forard with >display of followimg information: > > >Top solution : # 2 Dataset #1 >score: -1000 Fom: 0.19 sites:1 > > >Failed to carry out Autosol_score_ha_solutions: >list index out of range >STEP: Autosol_score_ha_solutions I'm sorry about this problem. I haven't seen it before, and I would like to track it down. I assume you are using version 1.24.1b, is that correct? If you would like to send me the data for this (as a .tar or .tgz file, renamed to ".txt") I will try it out on my computer. All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov 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.tbgenomics.org

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phase extension through phenix
by Pramod Kumar JRF 11 Aug '06

11 Aug '06

Hi all I have one more question. Is any way in phenix GUI through which i can do phasing to lowere resolution, further phase extension to higher resolution? Becouse, my SAD data with single SeMet in whole protein of 3.5 Ang which have somewhat better phases and FOM at 5.0 ang resolution than 3.5 Ang resolution. Is it possible through phenix? If anybody have any one can help me? Thanks in advance. Pramod Kumar, c/o Dr. Shekhar C. Mande Lab of structural biology Center for DNA Fingerprinting and Diagnostics ECIL Road, Nacharam, Hyderabad-500076 India

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SAD and autosol
by Pramod Kumar JRF 11 Aug '06

11 Aug '06

Hi all I am new user of the phenix. I am using autosol for the SAD data of the 3.5 Ang of resolution data of spacegroup P42212. After running autosol with all inputs , during Hyss autosol is not able to move forard with display of followimg information: Top solution : # 2 Dataset #1 score: -1000 Fom: 0.19 sites:1 Failed to carry out Autosol_score_ha_solutions: list index out of range STEP: Autosol_score_ha_solutions Thanks in advance Pramod Kumar, c/o Dr. Shekhar C. Mande Lab of structural biology Center for DNA Fingerprinting and Diagnostics ECIL Road, Nacharam, Hyderabad-500076 India

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a few questions
by Jianghai Zhu 06 Aug '06

06 Aug '06

Hi all, I have a structure refined to 2.5 A. After simulated annealing (start temp = 5000, cool rate = 25, final temp = 100, include TLS refinement and NCS restraint), my R and Rfree are 24.6% and 28.7% respectively. I then turned off the SA in the generated def file and carried on the combined refinement. My R and Rfree went up to 25% and 29.2% respectively. Why did the Rfree go up after refinement? In the remarks of the output pdb file, I have one line, "REMARK twinned : True". What does this mean? The RMSD of bonds and angles after either SA or combined refinement are about 0.006 and 0.851 respectively. Don't you guys think the geometry restraints are too tight? How do I change the weight in PHENIX? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3030 +++++++++++++++++++++++++++++++

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Autobuild peptide?
by ckielkop 02 Aug '06

02 Aug '06

Hi, We have a molecular replacement RNA structure with a bound peptide. I'd like phenix autobuild the peptide, because only a portion of it is bound and we'd like an unbiased, silicon opinion about what that portion is. It's not clear to me how to proceed with this in phenix- we have a beautiful electron density map from CNS, coordinates for the RNA portion, and peptide sequence. Thanks for any guidance! -- Clara L. Kielkopf Assistant Professor Biochemistry and Molecular Biology Johns Hopkins University Rm. W8708 BSPH 615 N. Wolfe St. Baltimore, MD 21205 Ph. 443-287-4546

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Build problems: 1.24.1b on SLES9
by Chris Richardson 01 Aug '06

01 Aug '06

Dear all, I've just been trying to install 1.24.1 beta on a new server running SuSE Linux Enterprise Server 9. The machine's a dual Xeon, so I've been using the 64-bit linux 2.6 build. I'm invoking install with ./install --prefix=/common/app/phenix-1.24.1b Installation fails with the message configuring PHENIX components Error configuring: see /common/app/phenix-installer-1.24.1b/ build-binary/intel-linux-2.6-x86_64/zaltu/log/binary.log for details Looking at the log file, the last few lines are ./iotbx/iotbx/shelx/from_ins.py ./iotbx/iotbx/shelx/write_ins.py ./ccp4io_502_cci/ ./ccp4io_502_cci/lib/ ./ccp4io_502_cci/lib/src/ ./ccp4io_502_cci/lib/data/ ./ccp4io_502_cci/lib/data/symop.lib ./ccp4io_502_cci/CCI_DIFFS python: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory SLES v9 uses libstdc++.so.5. Python works fine on this machine and is linked to libstdc++.so.5. I assume (probably incorrectly) that the error comes from some component of Phenix that is linked to the later version of the library. Does anybody have handy hints for installation on SLES? I would try it with SLES v10, but that would conflict with other packages we have running on that machine. TIA, Chris -- Dr Chris Richardson - sysadmin, Structural Biology Section, icr.ac.uk

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Problems running demo
by Miguel Ortiz Lombardia 01 Aug '06

01 Aug '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, Sorry if this kind of problems have been posted before, I tried unsuccessfully to find a relevant FAQ. I'm new to Phenix, so I thought it would be a good idea to run the GUI demo first. I installed, set up the programs and copied the data in a directory and did as instructed in the demonstration sequence page. I find two problems: 1. When I call the GUI I don't see the Tasks tab (well, perhaps not a problem, just a misunderstanding) 2. After I load the AutoSol wizard and press "Continue" the wizard doesn't turn to green. Instead, it remains blue and get this message in the console: (...) SUMMARY Input files dataset #1 peak.sca Creating new Data Storage /home/miguel/tests/phenix_demo/PDS/AutoSol.1 Traceback (most recent call last): File "/usr/local/phenix-1.24.1b/phenix/phenix/pds_server/ProcessMaster.py", line 269, in ? run() File "/usr/local/phenix-1.24.1b/phenix/phenix/pds_server/ProcessMaster.py", line 193, in run tasklist = strategyDataStorage.getObject(ProcessKey) File "/usr/local/phenix-1.24.1b/phenix/phenix/server/PDSClient.py", line 146, in getObject return self.loader(pickle_string) File "/usr/local/phenix-1.24.1b/phenix/phenix/server/PDSClient.py", line 27, in loader self.loader(pickle_string) File "/usr/local/phenix-1.24.1b/phenix/phenix/server/PDSClient.py", line 17, in loader return cPickle.loads(pickle_string) ValueError: could not convert string to float Any ideas of what may be wrong? Cheers, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: molatwork(a)yahoo.es www: http://www.ysbl.york.ac.uk/~mol/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (GNU/Linux) iD8DBQFEzgoeF6oOrDvhbQIRAn6SAJ4zmtiWyYJhmB7hdJeEGUp3kr0MtACfYffg ZvyFTX9ExvysvTOav35k0pg= =nS7A -----END PGP SIGNATURE-----

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