August 2012 - phenixbb - phenix-online.org

real space correlation
by Bradley Hintze 22 Aug '12

22 Aug '12

Hey Phenix team, I am trying to get real space correlation measurements for 1eao and ran into a problem. $ phenix.fetch_pdb --mtz 1eao $ phenix.real_space_correlation 1eao.pdb 1eao.mtz Multiple equally suitable arrays of observed xray data found. Possible choices: 1eao.mtz:FOBS,SIGFOBS 1eao.mtz:F(+),SIGF(+),F(-),SIGF(-) Please use .labels to specify an unambiguous substring of the target label. Looking in the options for phenix.real_space_correlation it is unclear how to specify the labels for the reflection file. Any assistance on this would greatly be appreciated. Thanks, Bradley -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry Please help me raise money for my ride to assist children with disabilities! <http://www.ridewithoutlimits.org/site/TR?px=1166331&pg=personal&fr_id=1260&…>

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autosol error
by Nora Cronin 21 Aug '12

21 Aug '12

Running phenix.autosol in input wavelength and f" and f' parameters are rejected as follows: "Guessing wavelength for mad is 1.0 Guessing scattering factors for PT at 1.0 A Removing wavelength_list from Facts as length does not match wavelength_list: [1.0721, 1.0538] input_file_list: ['/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_FP_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_F(+)_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_FP_rm.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_F(+)_rm.sca'] NOTE: you may need to select specific datasets from your input files with either group_labels_list (for a script) or peak.labels=xxxx (or similar, for command_line) Removing f_prime_list from Facts as length does not match f_prime_list: [-17.31, -15.31] input_file_list: ['/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_FP_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_F(+)_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_FP_rm.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_F(+)_rm.sca'] NOTE: you may need to select specific datasets from your input files with either group_labels_list (for a script) or peak.labels=xxxx (or similar, for command_line) Removing f_double_prime_list from Facts as length does not match f_double_prime_list: [11.93, 10.5] input_file_list: ['/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_FP_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_pk_editdname1_PHX_F(+)_pk.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_FP_rm.sca', '/dls/i03/data/2012/mx6385-40/processing/vvx/phenix/AutoSol_run_6_/xds_262_6_rm_editdname1_PHX_F(+)_rm.sca'] NOTE: you may need to select specific datasets from your input files with either group_labels_list (for a script) or peak.labels=xxxx (or similar, for command_line) Why is this rejection of input happening? what does "length does not match" indicate? Best Nora The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Reproducing a run in phenix.hyss
by Jeffrey, Philip D. 19 Aug '12

19 Aug '12

I've got an interesting potential S-SAD solution that crops up rarely in a script I was using to trawl parameter space in phenix.hyss. Since I was not optimistic of the outcome I did not save all output files. Hyss appears to use a random number generator and allows the seed to be specified on the command line, so is there any way to figure out what random number seed it used based on the information written to stdout while the program is running ? Merely running the command again does not trivially recreate the solution and egrep -i 'rand|seed' LOG only pulls out: Nigel Moriarty, Reetal Pai, Randy Read, Jane Richardson, David Richardson, time_log: p1_recycling random_omit: 990 1.49 0 0.00151 time_log: random_omit: 891 0.62 0 0.000696 Cheers Phil Jeffrey Princeton

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phenix.refine crash
by Maxime Cuypers 18 Aug '12

18 Aug '12

> > Hi, > > i am refining a neutron structure and i keep having this error: > > > File > "/usr/local/phenix-dev-1129/build/intel-linux-2.6/../../phenix/phenix/command_line/refine.py", > line 11, in <module> > command_line.run(command_name="phenix.refine", args=sys.argv[1:]) > File > "/usr/local/phenix-dev-1129/phenix/phenix/refinement/command_line.py", line > 146, in run > call_back_handler=call_back_handler) > File "/usr/local/phenix-dev-1129/phenix/phenix/refinement/driver.py", > line 1533, in run > ncs_manager = self.ncs_manager) > File > "/usr/local/phenix-dev-1129/phenix/phenix/refinement/strategies.py", line > 1109, in refinement_machine > h_params = h_params) > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 212, in __init__ > nproc = nproc) > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 315, in __init__ > result = self.try_weight(weight, print_stats=True) > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 401, in try_weight > minimized = self.minimize() > File > "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/refinement/adp_refinement.py", > line 470, in minimize > self.model.set_refine_individual_adp() > File "/usr/local/phenix-dev-1129/cctbx_project/mmtbx/model.py", line > 1231, in set_refine_individual_adp > iselection = selection_iso.iselection()) > RuntimeError: cctbx Internal Error: > /net/longnose/scratch2/phenix/phenix-dev-1129/cctbx_project/cctbx/xray/scatterer_flags.h(417): > CCTBX_ASSERT(f.use_u_iso()) failure. > > i see the last line is already a known issue as it was already posted in > phenixbb in 2010 but was perhaps solved offline. > > thanks in advance for any help (as i am really stuck) > > -- > Dr. Maxime Cuypers > Institut Laue Langevin (ILL), Deuteration lab > Rue Jules Horowitz, 6, BP 156 > 38042 Grenoble cedex 9 > France > > >

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Real-space and twin refinement
by Haim Rozenberg 13 Aug '12

13 Aug '12

Hello, We've just downloaded and install the new dev-1129 release of phenix hoping to be able to run RS refinement on our twin structures. According to the change log it should be possible with this version. ------------------------------------------------------------------------ Version 1.8.1 and nightly builds (TBA) ====================================== - phenix.refine: - overall B-cart now applied to individual atomic B-factors (restores pre-1.8 behavior) - improvements to torsion NCS rotamer correction - real-space refinement for twinned structures ------------------------------------------------------------------------ Unfortunately, while trying to run - through the GUI - phenix dev-1129 with our twin setting and the "Real space" option, the usual message popped up: "PHENIX error: Real-space refinement is not available for twinned structures." FYI, it runs just fine without the "Real-space" option. Did we have false hopes? Did we misunderstood? Is that a bug? All the best, Haim ============================================ Haim Rozenberg, PhD. Department of Structural Biology Kimmelman Building Weizmann Institute of Science 76100 Rehovot, Israel Phone: +972-8-9344289 FAX:+972-8-9344136 E-Mail: haim.rozenberg(a)weizmann.ac.il<mailto:[email protected]> ============================================ "Quis custodiet ipsos custodes?" D.I. Iuvenalis

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difficult phasing problem
by Ian Slaymaker 09 Aug '12

09 Aug '12

I am trying to solve the structure of a ~30kd monomeric protein for which we have 2.5A diffraction data, and a search model with ~65 % similarity (i have tried, homology models of this and others, as well as using sculpter to build several variations of core search models). I have tried all my possible space groups and a huge range of parameters, and mr_rosetta to rebuild some of my better (but still bad) MR solutions. My LLG is persistently negative (<-1000), which may be due to translational noncrystallographic symmetry which was identified by xtriage. We have unfortunatly been unable to phase this data with selmet SAD, so I am looking for some other MR things to try. Any suggestions for working with tNCS (if this is really the problem) would be much appreciated.

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test set count question
by Filip YABUKARSKI 08 Aug '12

08 Aug '12

Dear all, I am refining a structure with phenix.refine using a .mtz which contains F/SigF and DF/SigDF (CCP format from xdsconv) and i have something like 10000 unique reflections. The test set was created with the uniqueify script. If I understand correctly in the manual it is written that phenix.refine will separate the <F>/<SigF> into "F(+) SIGF(+) F(-) SIGF(-)), instead of keeping the original non-anomalous amplitudes". My question is about the "FREE R VALUE TEST SET COUNT" in the .pdb after phenix.refine. If I understand correctly the number for the test set will also be "doubled" because the <F> will be separated into F+ F-? Logically both F+/F- after separation are kept in the test set is this right? And an impair number for the test set in this case means that only the F+ OR F- was observed? Sorry if I ask a trivial question but I just want to be sure I am using the program in the right way Thanks in advance Filip

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Re: [phenixbb] test set count question
by Kay Diederichs 08 Aug '12

08 Aug '12

Dear Filip, concerning XDSCONV: if FRIEDEL'S_LAW=FALSE, using filetype of CCP4, you get F,SigF,DF,SigDF,isym using filetype CCP4_F, you get F,SigF,F(+),SigF(+),F(-),SigF(-) using filetype CCP4_I, you get IMEAN,SIGIMEAN,I(+),SIGI(+),I(-),SIGI(-) so you can (and should) directly output from xdsconv what you need for a downstream program. A short explanation is at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsconv Detailed explanation of each format is at http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xdsconv_formats.h… HTH, Kay

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changing a project directory
by Kendall Nettles 08 Aug '12

08 Aug '12

Dear PHENIX developers, I want to migrate my PHENIX project directories. I moved one project directory as a test, and the GUI doesn't give an opportunity to relocate, which would be a nice feature. Is there a way to edit their location for the PHENIX GUI? Kendall

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two problems about phenix.mr_rosetta
by chen c 08 Aug '12

08 Aug '12

Dear all: I've collected a data set for my crystal, which is a two-protein complex. However, normal molecular replacement method gives no solution and thus didn't work. Right now I'm struglling with the phenix.mr_rosetta method. However, I've got several problems when reviewing it, and thus looking forward to get some advice here. 1: There are such words *"NOTE 2: If your structure contains more than one chain or requires more than one homology model to represent the structure, then you need to use mr_model_preparation and phenix.automr to place your model. Then you can start phenix.mr_rosetta with already_placed=True**"* in phenix documentation page. My understanding for this sentences is: the solution derived from *automr* is treated as an original searching model for phenix.mr_rosetta, in which case, we should add the command line *"run_prerefine=True \ number_of_prerefine_models=1000"*. However, what is *mr_model_preparation * for? And if no solution is given by *automr*, what should I do? What's more important, why not endow the phenix.mr_rosetta program to be capable of dealing with data set from multi-chain protein complexes? Since I thought the idea of preliminary manipulation by the program *automr* would decrease the power of *phenix.mr_rosetta*. 2: Two .hhr files are produced. But as displayed in the phenix.mr_rosetta documentation page, only one .hhr file like *"hhr_files=bfr258e.hhr"* are listed in the command line. Why? Could somebody give me any advice on this, please? Thank you and best regards chen -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China -

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