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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 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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