- phenixbb - phenix-online.org

mr_rosetta and Condor
by Dmitry Rodionov 06 Sep '12

06 Sep '12

Good day! I am trying to get a bunch of OS X 10.6 workstations managed by Condor to work together on an mr_rosetta project. I am new to batch systems and rather confused. The Phenix manual states: "Single file system required for mr_rosetta All files are stored on a single file system that must be accessible to all jobs." What exactly has to go on the network share and how would I make the execution nodes aware of it? Could somebody please share some information on a working setup of this sort? Thanks! Best regards, Dmitry

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phenix/ccp4 monomer library compatibility
by Wulf Blankenfeldt 05 Sep '12

05 Sep '12

Dear all: this may have been asked a thousand times, but: are the ccp4 standard monomer libraries incompatible with phenix.refine, and if yes, is there an easy way to resolve this? I am refining a structure with an FMN, which I build with the "get monomer" option in coot. Unfortunately, phenix.refine doesn't like it and throws it out. Using a cif generated with elbow, on the other hand, has chirality errors (which I can fix...) and isn't liked by coot (0.6.2), which refuses to refine the ligand. Thanks in advance for your help, Wulf -- Prof. Dr. Wulf Blankenfeldt NW-I, 2.0.U1.09 Universitaet Bayreuth fon: +49-(0)921-55-2427 Lehrstuhl fuer Biochemie fax: +49-(0)921-55-2432 Universitaetsstrasse 30 e-mail: wulf.blankenfeldt [at] uni-bayreuth.de 95447 Bayreuth web: www.biochemie.uni-bayreuth.de Germany

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B factor refinement in recent versions of phenix
by "Weiergräber, Oliver H." 31 Aug '12

31 Aug '12

Hello, I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine. The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00! There are no obvious abnormalities in the electron density, and R values are quite good. I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A². So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8. I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems. Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab. Any ideas what might be causing this and how to revert to the original behavior? Thanks in advance Oliver ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Kennen Sie schon unsere app? http://www.fz-juelich.de/app

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Phaser and PTNCS - bug fixed in latest builder for Phenix?
by Rafael Lemos Miguez Counago 29 Aug '12

29 Aug '12

Dear all, I noticed on the Phaserwiki webpage (news section) that there is a bugfix (dated 14th of August/2012) for Phaser as the "Packing test was incorrectly applied to reoriented molecules where there was PTNCS". I had a look in the "changes" file, but could not find if this bugfix is part of the latest Phenix installer (dev-1143) or not. Could anybody clarify this point for me? Thanks a lot. Best wishes, Rafael.

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AsCA 12/CRYSTAL 28 Conference and the Bragg Symposium - Early Bird Registration closes this weekend
by John Bruning 29 Aug '12

29 Aug '12

Dear All, Early bird registrations for the Asian Crystallography Association Conference and the Bragg Symposium close this Saturday. You can register for one or both events. **** ** ** The one-day Bragg Symposium on Thursday the 6th of December may be of particular interest as it will specifically address the scientific and historical aspects associated with the centenary of Lawrence Bragg’s explanation of X-ray diffraction. ** ** To register, visit: **** ** ** http://www.sapmea.asn.au/conventions/crystal2012/index.html Kind regards to read this newsletter in your browser click here <http://www.sapmea.asn.au/conventions/crystal2012/emails/enews_01.html>**** [image: cid:[email protected]]**** AsCA 12/CRYSTAL 28 *Conference Newsletter***** Volume 1, May 2012**** Invitation to attend**** *A Joint Meeting of the Asian Crystallographic Association (AsCA), ** Society of Crystallographers in Australia and New Zealand (SCANZ) and the BRAGG Symposium, * November 2012 marks the centenary of the founding of X-ray crystallography by Lawrence Bragg, a field in which he and his father, William, made pre-eminent contributions that were recognised by the award of the Nobel Prize for Physics in 1915. William was the Elder Professor of Physics at the University of Adelaide from 1886 to 1909 and Lawrence was born and educated in Adelaide.**** To celebrate this important anniversary, the legacy of the Braggs’ discoveries in X-ray crystallography and the insights that they have provided into the structure of matter, a combined scientific meeting of the Asian Crystallography Association and the Society of Crystallographers in Australia and New Zealand is to be held in Adelaide from the 2nd to 5th of December 2012. The Conference will be followed by the Bragg Symposium at the University of Adelaide on the 6th of December 2012 that will explore some of the historical context and personal links to the Braggs' work as well as present some of the broader scientific and social impacts of the Braggs' work. The Conference and Symposium will have a strong line-up of national and international speakers.**** Call for Abstracts**** For more information and online abstract submissions please click here: http://www.sapmea.asn.au/conventions/crystal2012/abstracts.html**** Online Registration:**** For more information on online registration and accommodation bookings please click here: http://www.sapmea.asn.au/conventions/crystal2012/rego.html **** **** Conference Secretariat**** [image: cid:[email protected]]**** *sapmea* Unit 12 202 Glen Osmond Rd Fullarton SA 5063 Phone: (08) 8274 6059 Fax: (08) 8274 6000 crystal2012(a)sapmea.asn.au**** ** ** ** **

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Funky message on phaser MR
by Rafael Lemos Miguez Counago 28 Aug '12

28 Aug '12

Dear all, I am getting this message when running Phaser-MR in Phenix (1.8-1069): "Warning: Resolution of data does not achieve (half) expected LLG target: placement of one/first ensemble will be very difficult" The data scales/merges OK. – 99% complete at 2.2A, Rmerge 8.4%. TNCS is detected by Xtriage and Phaser tries to account for that. Coincidently (?) my molecular replacement solution is not looking very good. Any ideas? Best wishes, Rafael.

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HB_score in Ligand Identification
by Brad C. Bennett 23 Aug '12

23 Aug '12

Hello to all- Where can I find a description of what "HB_score" is and how it is calculated in the Ligand Identification program in Phenix? I'm assuming this is a metric for hydrogen bonding capability/propensity of a fit ligand based on distance and angle to model atoms. I have an output rank list of the top 20 ligand fits, ranked by Z-score. The HB_score is all over the place: low = -0.59, high = 77.96, most are between 0-10. I think I understand the correlation coefficient and Z-score but how does the HB_score fit in with these? I can't find this in the documentation or in the Terwilliger et al. (2007) Acta D reference. Somehow I've "lost" the log file, so maybe the information is in there. Thanks in advance! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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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 22 Aug '12

22 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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refining multiple conformations
by Kendall Nettles 08 Aug '12

08 Aug '12

Hi, We have a structure with the ligand showing two overlapping conformers. When we refine it with both conformers separately, it is pretty clear that there are substantial differences in the protein as a result, for about a third of the protein chain. My question is, would it be better to try to define altloc for those specific regions, or would it be OK to refine with two entire alternate protein chains? There is also a second protein chain that shows only a single binding mode for the ligand. It's a 2.0 angstrom structure with 4000 atoms and 27,000 reflections. The yellow map goes with the green model in the attached pic. Also, do we want to let each amino acid have its own occupancy? or should one ligand copy and one chain all have the same occupancy? I'm leaning towards the latter since the differences should be directly tied to the ligand binding mode. Kendall Nettles [cid:[email protected]]

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mr_rosetta problems
by Ian Slaymaker 07 Aug '12

07 Aug '12

I am trying to get mr_rosetta working on our cluster and am running into some problems I am not sure how to solve. The phenix_regression.wizards.test_command_line_rosetta_quick_tests tests went smoothly were completed. However, my first test run with all the defaults (not submitted to multiple processors) using my reflection file, HHR analysis file, sequence file, and the 2 fragment files failed with the below errors. I checked all the files, and it seems this is a problem with the fragment files but I am not sure exactly what they are supposed to look like. I thought it could be because our cluster doesnt have access to any outside networks...is this a problem with rosetta not being able to download pdb files? if so, is there a way to supply them internally? The aligned model looks somewhat what I expected it to (same beta sheet arrangement) but it seems to be incomplete. Any help would be very much appreciated! Splitting work into 100 jobs and running with 1 processors using sh background=None in /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1 Starting job 1...Log will be: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log ******************* ERROR ENDING *************** mr_rosetta failed... ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log : to match the actual PDB sequence: (protein sequence) New alignment line 4 for PDB: (protein sequence) Start position of target sequence in sequence file: 0 Aligned model for comparison: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/aligned_model.pdb Log for rebuilding: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log **************ERROR ENDING********************** Failed to run REBUILD...see log file in /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log The rebuild log had repeats of several errors that I am not sure how to address: core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 3 (repeated several times) core.fragments.ConstantLengthFragSet: line too short: Skipping line ' (repeated several times) core.fragments.ConstantLengthFragSet: finished reading top 0 0mer fragments from file/dataFiles/aat000_03_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug none 1

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Ordered solvent distances
by Abhinav Kumar 03 Aug '12

03 Aug '12

Hi, The default minimum distance that a water gets placed near protein/water atoms using 'ordered_solvent=true' option in phenix.refine is 1.8. Isn't this too close? Also, if two waters can't get placed in the density due to distance criterion, can phenix place one water in dual conformations in that density? -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992

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Lost my job history, can it be recovered? (GUI)
by Andrew Waight 02 Aug '12

02 Aug '12

Hello All, It just so happened that my lab's server ran out of space (someone else uploading datasets) while my phenix rosetta MR job was running. Now the GUI no longer shows any job history in the job history tab (although on the title page the number of jobs is correctly displayed. I cannot find any information on how or if its possible to recover my job history in the GUI. Any tips? Thanks so much. Drew

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July 2012 Computational Crystallography Newsletter
by Nigel Moriarty 31 Jul '12

31 Jul '12

Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles ----------- cctbx tools for transparent job execution on clusters On the analysis of residual density distributions on an absolute scale Short communications -------------------------------- DETAC: tools to detect alternative conformations by unrestrained refinement ERRASER, a powerful new system for correcting RNA models Fitting tips - Rotamer correction with backrub -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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what installer would work with a cluster with Darwin 9.8.0 if any?
by Tatyana Sysoeva 27 Jul '12

27 Jul '12

Hi all, I am starting to use a new computer cluster and just found out by uname that it runs Darwin OS? It is totally new to me and I am wondering if Phenix would run on it? should I use just some Mac installer? I would really appreciate any advices! Thank you! Sincerely, Tanya

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Re: [phenixbb] what installer would work with a cluster with Darwin 9.8.0 if any?
by Tatyana Sysoeva 27 Jul '12

27 Jul '12

Thank you Miguel and Ben! I did found the newest release at the cluster after I learned how to use "find" properly! In particular, thank you for pointing out the script to source! Best regards, Tanya

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refinement problem
by Afshan Begum 27 Jul '12

27 Jul '12

Dear Experts I am refining my structures in windows mode and every time i got this crash message i do not know how to solve this issue? If any one encountered this problem kindly suggest me how to solve it. While when i refine with refmac the file proceeds smoothly but i want to refinement in phenix due to utilize some parameters. its end like this: Exporting results ============================== Writing refined structure to PDB file: C:\Documents and Settings\pc user\Desktop\Refine_2\jbu_refine_2.pdb n_use = 7514 n_use_u_both = 7514 n_use_u_iso = 0 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 331 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 7514 After that its not produce the map file and gave errore crash mesage. <module> Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Your suggestion highly obliged I would be very thankful to you AFSHAN

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