- phenixbb - phenix-online.org

GRC on Diffraction Methods in Structural Biology
by Andrew Leslie 09 May '08

09 May '08

There is still time to apply to attend this GRC, relevant to researchers interested in Methods Development - details below! The official closing date is 22nd June, but places are limited to a total of 125. Best wishes Elspeth Garman and Andrew Leslie Gordon Research Conference on Diffraction Methods in Structural Biology July 13-18, 2008, Bates College, Lewiston, Maine, USA Co-Chairs: Elspeth Garman & Andrew Leslie The 2008 Gordon Research Conference on Diffraction Methods in Structural Biology will encompass advances in the methodology for macromolecular X-ray crystallography, and other diffraction/scattering applications. The full confirmed programme and timetable for the meeting can now be found below and at: http://www.grc.org/programs.aspx?year=2008&program=diffrac as well as details on how to register (registration closes on 22nd June 2008 but attendance is limited to 125 researchers). All macromolecular crystallographers interested in Methods development are encouraged to apply. To promote a lively meeting, we hope that all participants will present a poster and contribute to the discussions. *Confirmed Program as at 8th May 2008.* *MACROMOLECULAR STRUCTURES: PUSHING THE BOUNDARIES * Discussion Leader: *Janet Smith* (University of Michigan at Ann Arbor, USA) *Jens Preben Morth* (Aarhus University, Denmark) "Structure determination of the sodium-potassium pump" *Jack Johnson* (Scripps Research Institute, USA) "Crystallography of Viral Maturation Intermediates: Large Unit Cells, Particle Dynamics, and Energy Landscapes" *EXPERIMENTAL ASPECTS* Discussion Leader: *James Holton* (University of California, Berkeley, USA) *Douglas Juers* (Whitman College, USA) "Rational approaches to cryo-crystallography protocols" *Zbyszek Dauter* (Frederick Cancer Institute, USA) "A thoughtful approach to data collection" *Eddie Snell* (Hauptman-Woodward Medical Research Institute, USA) "Are X-rays damaging to structural biology? A case study with xylose isomerase" *Martin Weik* (Institut de Biologie Structurale, Grenoble, France) "Temperature-controlled cryo-crystallography to study the structural dynamics of proteins" *COMPLEMENTARY TECHNIQUES* Discussion Leader: *Peter Kuhn* (Scripps Research Institute, USA) *Junko Yano* (Lawrence Berkeley National Laboratory, USA) "Combination of XAS and XRD for studying a high-resolution structure of the photosynthetic water-splitting catalyst" *Dean Myles* (Oak Ridge National Laboratory USA) "New opportunities for neutron structural biology" *Carrie Wilmot* (University of Minnesota, USA) "Single crystal spectroscopy coupled to crystallography" *FUTURE DIRECTIONS IN SYNCHROTRON BASED MACROMOLECULAR CRYSTALLOGRAPHY * Discussion Leader: *Elizabeth Duke* (Diamond Light Source, UK) *Soichi Wakatsuki* (KEK, Japan) "Microfocus and low energy PX developments looking towards next generation synchrotron sources" *Ed Mitchell* (ESRF, Grenoble, France) "Bigger, better, faster, more: The ESRF Upgrade Programme" *Aina Cohen* (SSRL, USA) "Automation, Robotics and Remote Access at the SSRL Protein Crystallography Beam Lines" *Frank von Delft* (Structural Genomics Consortium, Oxford, UK) "A User's Wish: An Experiment-Focussed Beamline Interface" *EMERGING TECHNOLOGIES* Discussion Leader: *Andrew Leslie* (MRC-LMB, Cambridge, UK) *Robert F. Fischetti* (GM/CA-CAT, Argonne National Laboratory, USA) "Where have all the photoelectrons gone?" *Clemens Schulze-Briese* (Swiss Light Source, Villigen, Switzerland) "PILATUS 6M - the first year of regular user operation" *COMPUTATIONAL METHODS* Discussion Leader: *Airlie McCoy* (University of Cambridge, UK) *Sasha Popov* (ESRF, Grenoble, France) "BEST SAD data collection" *Paul Adams* (Lawrence Berkeley Laboratory, USA) "Automated structure solution with PHENIX" *Kevin Cowtan* (University of York, UK) "The 3 R's of automated model building: R-factors, resolution, and refinement" *George Phillips* (University of Wisconsin-Madison, USA) "Interpretation of electron density maps from protein crystals" *CHALLENGING PROBLEMS / MEMBRANE PROTEINS * Discussion Leader: *Tom Terwilliger* (Los Alamos National Laboratory, USA) *Chris Tate* (LMB-MRC Cambridge, UK) "Thermostabilisation and structure determination of a beta1 adrenergic receptor" *Mike Lawrence* (The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia) "Pursuit of the structure of the human insulin receptor ectodomain" *Mark Mayer* (NIH, Bethesda, USA) "Structure and function of allosteric ion binding sites in glutamate receptor ligand binding domains" *TALKS SELCETCED FROM POSTERS* *VALIDATION* Discussion Leader: *Ana Gonzales* (Stanford Synchrotron Radiation Laboratory, USA) *Gerard Kleywegt* (University of Uppsala, Sweden) "Validation" *Jane Richardson* (Duke University, USA) "MolProbity Progress: RNA, Auto-corrections, and H redux" *IMAGING METHODS OF THE FUTURE* Discussion Leader: *Raimond Ravelli* (Leiden University Medical Centre, The Netherlands) *Steve Ludtke* (Baylor College of Medicine, Houston, USA) "Resolution and Molecular Motion, Frontiers in CryoEM" *Carolyn Larabell* (Lawrence Berkeley National Laboratory) TBA

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Re: [phenixbb] mtz test set
by Ralf W. Grosse-Kunstleve 03 May '08

03 May '08

Hi Mark, > yes. however arp/warp has lost this ability in the ccp4i "classic" > mode. Oh, too bad. I wrote a small mtz_free_flipper.py script that will be part of the next CCI Apps maintenance release (hopefully tomorrow). If you want to use it right now, get the current cctbx bundle from here: http://cci.lbl.gov/cctbx_build/all.html Build tag: 2008_05_02_0119 (or later) Pick a bundle from the "cctbx+Python" column. You can install it anywhere, e.g. in /var/tmp/junk. After the perl cctbx*.selfx command is finished (a few seconds), source the setpaths script for your shell as usual, then run this command: cctbx.python cctbx_sources/iotbx/iotbx/examples/mtz_free_flipper.py your.mtz It will write a file free_flipped_your.mtz. The script assumes the R-free flags column label is "R-free-flags". If your label is different, copy the example script, modify the label (should be obvious) and run the modified script: cctbx.python copy_of_mtz_free_flipper.py your.mtz Note: the script will not work with the current CCI Apps because I had to add something to the mtz module last night to keep the script simple. Ralf

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model bias: phaser + prime-and-switch VS simulated annealing in phenix VS simulated annealing in cns + prime and switch
by hari jayaram 02 May '08

02 May '08

First off sorry for the cross post across bbs I have a molecular replacement solution for a single site mutant for data that goes out to 2.8 A. After molecular replacement in phaser I run the following and examine the maps for bias from the model. Option1: simluated annealing refinement in phenix using the phaser mtz Option2: take the phaser mtz and then just run prime and switch in resolve and look at the map Option3: First part: take the phaser mtz and then run simulated annealing and sigmaa in cns 1.2.2 . Second part: Run prime-and-switch using part1s model phases and modified Fs I am observing that Option 1 and Option 2 the maps are indistinguishable from each other and show very little bias from the model. In Option 3 just cns simulated annealing does not go as far at removing bias as cns simulated annealing plus prime-and-switch. Although my estimate of model bias is just a "look and see" feeling. Since I lack a thorough understanding of the relative merits of these algorithms I have the following questions 1)Does simulated annealing refinement as implemented in phenix use a prime-and-switch style approach to modify phases at any point to guide the refinement 2) Am I wrong in assuming that just simulated annealing and sigma-aa weighted maps for cns (Option 3 part 1) are not as good as cns simulated annealing + sigmaa+ prime_and_switch ( option3 part 2) Hoping to get a better idea on how well these approaches fair at removing model bias Hari Jayaram Postdoc , Brandeis University

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pseudo-translational symmetry refinement
by a a 02 May '08

02 May '08

Dear all: We have a set of crystal data having psuedo-translational symmetry when examined with xtriage: ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - <I^2>/<I>^2 : 2.519 - <F>^2/<F^2> : 0.724 - <|E^2-1|> : 0.854 - <|L|>, <L^2>: 0.504, 0.337 Multivariate Z score L-test: 1.854 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. No (pseudo)merohedral twin laws were found. Patterson analyses - Largest peak height : 67.742 (corresponding p value : 4.897e-06) The analyses of the Patterson function reveals a significant off-origin peak that is 67.74 % of the origin peak, indicating pseudo translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo translational symmetry is equal to the 4.8972e-06. The detected tranlational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. ------------------------------------------------------------------------------- The structure was solved by auto-sad at 2.7A. However, the r-factor can not be lowered by phenix.refine (TLS+ADP+rigid). Is there any manipuliations we can do to deal with this situation? Thanks, Zhiyong Ren, MD Anderson Cancer Center ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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mtz test set
by Mark Collins 02 May '08

02 May '08

Hi Everyone, How can I get foo.mtz in which the test set number for R-free is 0 and the working set is say 1. Thanks Mark

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autosol output to electron density figure in pymol
by shivesh kumar 02 May '08

02 May '08

Dear all, I have an overall_best.pdb and overall_best_refine_map_coeffs.mtz file as an output file from Autosol.When I open this in coot I see the nice density.How can make a figure with density using pymol.Thanx in advance for the suggestions. Shivesh

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Re: [phenixbb] native Patterson peak
by Peter Zwart 02 May '08

02 May '08

31 is not too bad actually. When you have such a PT peak, I would consider only an even number of copies in the ASU. When entering desperate mode, I would try all possible P2x2y2z flavors even though your systematic absences might be clear. Of course, experimental phases could be a good solution. HTH P 2008/5/1 David Garboczi <dgarboczi(a)niaid.nih.gov>: > We have datasets measured on crystals of a 19 kD protein that are > P212121, with cell constants of 66, 75, 136. > > Matthew's considerations say 3, 4, or 5 copies per au are probable. > > xtriage finds a native peak at (0.0, -0.5, 0.036) that is 31 in > height (origin=100) > > No self-rotation function peaks in xprep, that I can understand. > > Is this clearly translational symmetry that is making MR difficult? > > Hints as to how to go forward are welcome. > > thanks, > > Dave > > > -- > David N. Garboczi, PhD > Phone: 301-496-4773 > Investigator, Structural Biology Section (SBS) > Laboratory of Immunogenetics (LIG) > National Institute of Allergy and Infectious Diseases (NIAID) > National Institutes of Health (NIH) > Twinbrook 2/Room 110 > 12441 Parklawn Drive > Rockville, Maryland 20852-1742 > Fax: 301-402-0284 > Email: dgarboczi(a)niaid.nih.gov > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Re: [phenixbb] [ccp4bb] Need Solve/Resolve advice [shameless crosspost to phenixbb]
by Peter Zwart 01 May '08

01 May '08

Hi, (sorry for the crosspost / jumping between bb's), but I don't like advertising phenix on the ccp4bb. If new to Solve (or old as well), try using phenix.autosol. The gui is relatively intuitive, the command line (at least for SAD) as simple as possible and the documentation is very thorough. Before running autosol, try running xtriage and find out if you have translational pseudo symmetry. If you have more then a single molecule in the ASU, there will be NCS, unless all molecules have *extremely* different conformations. The NCS might not be proper/closed though. HTH Peter 2008/4/30 Megan Guelker <megdg(a)rice.edu>: > CCP4bb subcribers, > > I am a new user to Solve/Resolve and am using it on a Mad dataset. Solve > outputs three sites: > > pdb coordinates fractional coordinates > -15.833 35.392 38.440 0.0486 0.4315 0.1615 > 7.834 76.449 38.475 0.5487 0.9320 0.1617 > 16.310 60.866 37.449 0.5432 0.7420 0.1574 > > I noticed that the fractional coordinates for the first two sites are > separated by 0.5 units in x and y, and they appear to be the same site from > looking at the density surrounding them. I know that Solve can output some > sites with repetition if they are results from different seeds. > > I have tried running Solve again with ADDSOLVE and these sites as input (all > three and combinations of the three) and have not been able to pull out any > additional sites. I have also tried using various resolution ranges for > Solve. The same three sites are always output. > > The FOM for the map produced by Solve is 0.45. Resolve improves the FOM to > 0.66. > > The protein has 148 aa with 4 Se sites per protein. The crystals are in > space group P3221, and there are six copies per asymetric unit. There is no > non-crystallographic symmetry. > > I am a new user to Solve, and haven't been able to find an explanation for > why the output sites are so similar and separated by 0.5 units. Does anyone > have any experience with this type of result? I would appreciate any input > and suggestions on how to locate additional sites. > > Thank you for your consideration, > Megan Guelker > > -- > Megan Guelker > Graduate Student > Rice University > Department of Biochemistry & Cell Biology > 6100 Main St. - MS 140 > Houston, TX 77005 > 713-348-2492 (lab) > megdg(a)rice.edu > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Refining low resolution structure
by Humberto Pereira 30 Apr '08

30 Apr '08

Dear all I was trying to refining a low resolution structure with Phenix. The crystal belongs to the SG P6122 with one monomer per ASU. The monomer contains approximately 270 residues. There isn't any NCS operators. The crystal diffracts up to 4.0 Angstrons, with good statistics, however I have only 4204 unique reflections. I solved the structure by MR by Phaser and the solution was quite reasonably. Initially I performed a phenix refining cicle with SA + rigid body, however the Rs values is very divergent (43 and 59%), so I decided to use the key xray_data.r_free_flags.ignore_r_free_flags=true in order to save my precious reflections with and without SA, and I also use the group_adp., in those cases the R is about 39-40%. I want a help to decide the best refinement strategies for low resolution refinement with phenix. BTW I'm trying to produce some different constructions of the gene, expecting improve the resolution. Thanks Humberto

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optimize_wxc won't run
by Nian Huang 30 Apr '08

30 Apr '08

Dear All, I am a novel phenix user. There is a problem whenever I use option optimize_wxc in phenix. The error message looks like following, ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' I don't know what's the problem. Could it be my installation? Nian Huang, Ph.D. Dept. of Biochemsitry UT Southwestern Medical Center

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