- phenixbb - phenix-online.org

Integrated Structural Biology, PhD program at the IGBMC
by Alexandre OURJOUMTSEV 21 May '14

21 May '14

Dear all, kind reminder for PhD fellowship opportunities at the International PhD program of the IGBMC, notably for Integrated Structural Biology. Deadline for applications is 3rd of june 2014: http://phdprogramme.igbmc.fr/ Interested candidates are invited to visit the home pages of the teams of the Integrated Structural Biology department at http://www.igbmc.fr/research/department/3/ Please feel free to contact the group leaders for further information about the projects. Best regards, Bruno Klaholz Sacha Urzhumtsev

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any idea what is this? (unidentifiable blob in electron density map)
by Murpholino Peligro 21 May '14

21 May '14

1) 2FOFCWT PH2FOFCWT bue map (front1.png) (process: XDS->Aimless within CCP4i->MR with Phaser->Phenix.refine/coot->Phenix-refine-withwaters/coot) 2) FWT PHWT purple map (front2.png) (Output from Aimless and calculate Fs with refmac within coot with last pdb from 1st line) What do I have in the crystal? NaCl, Sodium acetate, water, lysozyme and some complexes (~ 400 daltons) that chelate Cu2+ Is there like a gallery of crazy-looking blobs that are explained with something ....real and possible? (that would be great help for the newb) Thanks in advance. links to screenshots right here: https://www.dropbox.com/s/rzjepvr8genolxi/front1.png https://www.dropbox.com/s/0iycf4lh5y726x4/front2.png https://www.dropbox.com/s/xx5kvgn91p763ei/faraway.png (1.0 rmsd for both maps above and 3.5 for the "red and green maps")

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phenix.rna_validate and the MolProbity web server report different bond angle violations
by Huw Jenkins 20 May '14

20 May '14

Hi, I’ve recently been using phenix.erraser to help correct RNA geometry errors and finding it very useful. However, it appears that the geometry validation statistics reported by phenix.rna_validate with respect to bond angle outliers are very different from those reported by the MolProbity web server. As an example - if I run phenix.rna_validate on 1u8d (as used in the documentation for phenix.erraser) the following outliers are reported: RNA Validation ----------------------------------------------- Pucker Outliers: #residue:delta_angle:is_delta_outlier:epsilon_angle:is_epsilon_outler G A 15 :74.054:no:103.458:yes U A 48 :119.081:yes:283.965:no U A 63 :90.366:yes:74.220:yes ----------------------------------------------- Bond Length Outliers: #residue:atom_1:atom_2:num_sigmas ----------------------------------------------- Angle Outliers: #residue:atom_1:atom_2:atom_3:num_sigmas C A 39 : C5': C4': C3':-5.294 U A 63 : O3': C3': C2':-4.402 ----------------------------------------------- Suite Outliers: #suiteID:suite:suiteness:triaged_angle G A 16 :!!:0.000:epsilon-1 U A 48 :!!:0.000:delta U A 49 :!!:0.000:delta-1 A A 64 :!!:0.000:epsilon-1 The MolProbity web server reports the same pucker and suite outliers but flags up many more angle violations: A 39 C worst is C5'-C4'-C3': 10.588 σ A 63 U worst is O3'-C3'-C2': 8.803 σ A 54 C worst is C5'-C4'-C3': 7.883 σ A 49 U worst is C2'-C1'-N1: 5.416 σ A 62 G worst is C2'-C1'-N9: 4.946 σ A 15 G worst is O3'-C3'-C2': 4.825 σ A 22 U worst is C5'-C4'-C3': 4.785 σ A 64 A worst is C4'-C3'-O3': 4.648 σ A 65 A worst is C2'-C1'-N9: 4.582 σ A 44 A worst is C4'-C3'-C2': 4.395 σ As the number of sigmas for the angle violations are different between phenix.rna_validate and MolProbity I guess they’re using different target distributions (not just reporting at a different sigma cut-off) but I’ve no idea which is more valid. Hopefully there is a simple explanation! Thanks, Huw

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Postdoctoral Fellow: Data Processing and Merging in Serial Crystallography
by Kay Diederichs 19 May '14

19 May '14

The Paul Scherrer Institute PSI is the largest research centre for natural and engineering sciences within Switzerland. We perform cutting-edge research in the fields of matter and materials, energy and environment and human health. By performing fundamental and applied research, we work on sustainable solutions for major challenges facing society, science and economy. PSI is committed to the training of future generations. Therefore about one quarter of our staff are post-docs, post-graduates or apprentices. Altogether PSI employs 1900 people. The Swiss Light Source (SLS) is one of the most advanced radiation sources worldwide. The SLS Macromolecular Crystallography Group operates two high performance undulator beamlines as well as a state-of-the-art bending magnet beamline for protein crystallography. The group is involved in several aspects of protein crystallography including the development of advanced beamline instrumentation and crystallographic methods, as well as structural biology projects in collaboration with the Biomolecular Research Group at PSI and external partners. In collaboration with Prof. Kay Diederichs at University of Konstanz, we are looking for a Postdoctoral Fellow: Data Processing and Merging in Serial Crystallography Your tasks ========== * Serial crystallography with bright micro-focused X-ray beams from both synchrotron and free electron laser sources has brought new opportunities in micro- and nanocrystallography. At the same time, obtaining best diffraction data from hundreds and thousands of crystals presents unprecedented challenges. New statistics based method of multi-crystal merging and analysis need to be developed and validated. * Develop multi-crystal data analysis, processing and merging methods for serial micro- and nanocrystallography at synchrotron radiation (SR) and X-ray free electron laser (XFEL) sources * Actively participate in serial crystallography experiments at both SR and XFEL sources * Implement an automated data merging pipeline at the SLS protein crystallography beamlines Your profile ============ You hold a PhD degree in (bio-)chemistry or physics and have several years of experience in protein crystallography. Working knowledge for data processing programs is a must. Experience in computer programming would be a significant advantage. If you are a good team player with good communication skills and sense of responsibility, this position will offer a great opportunity for you to develop your research career in an exciting and highly multidisciplinary environment. For further information please contact Prof. Kay Diederichs, phone +49 7531 88 40 49 or Dr Meitian Wang, phone +41 56 310 41 75. Please submit your application online (including list of publications and addresses of referees) for the position as a Postdoctoral Fellow (index no. 6112-00) to: Paul Scherrer Institute, Human Resources Management, Miriam Zehnder, 5232 Villigen PSI, Switzerland http://www.psi.ch/pa/offenestellen/0789-1 -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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Sharing a Phenix project via Dropbox
by Derek Logan 19 May '14

19 May '14

Hi, Has anyone ever successfully shared a Phenix project through Dropbox? I tried Googling for info on this without success. I have tried sharing but it doesn't work because Phenix uses the full path to the project, e.g. /Users/derek/Dropbox/project rather than ~/Dropbox/project, which would work for all users sharing the project. I tried manually editing project.phil in the .phenix directory, but at the end of a run of phenix.refine it was overwritten again. Is there somewhere (job_history.phil?) I can replace /Users/derek with ~ so that it the change will be permanent? I think that this would be a very effective way for me to set up a project being run by one of my PhD students involving people from at least 3 labs that could have opinions on the refinement! /Derek P.S. We are all using Macs.

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phenix.real_space_refine
by Gino Cingolani 15 May '14

15 May '14

Hi all, I'm trying to refine a pdb against an EM map using phenix.real_space_refine using default parameters (e.g. phenix.real_space_refine model1.pdb map.ccp4). The program starts OK but quickly stops with the following output (see below) Any thoughts? Thanks so much! Gino ########################################################################### Add C-beta restraints ********************* Adding C-beta torsion restraints... num c-beta restraints: 11832 ------------------------------------------------------------------------------- Getting target map ****************** Traceback (most recent call last): File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 494, in <module> o = run(sys.argv[1:]) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 273, in __init__ self.caller(func = self.get_target_map, prefix="Getting target map") File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 298, in caller func(prefix=prefix) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 372, in get_target_map number_of_macro_cycles = self.params.refinement.macro_cycles) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 153, in extract_target_map_data_and_crystal_gridding crystal_symmetry = inputs.xray_structure.crystal_symmetry()) File "/usr/local/phenix-dev-1615/cctbx_project/mmtbx/utils/__init__.py", line 3094, in structure_factors_from_map use_sg = True) File "/usr/local/phenix-dev-1615/cctbx_project/cctbx/miller/__init__.py", line 1309, in structure_factors_from_map assert map.focus_size_1d() > 0 and map.nd() == 3 and map.is_0_based() AssertionError ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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NCS in mr_rosetta
by Stefan Knight 15 May '14

15 May '14

Hi, Is there some way to make mr_rosetta use information about NCS present in the data? I have data from a crystal in sg P21 with a clear 3-fold axis perpendicular to the two-fold screw (as seen in self rotation function), and most likely 6 molecules in the asymmetric unit, but none of the mr_rosetta solutions that have appeared so far show 3-fold symmetry, and it doesn’t seem like the ncs is used in the search. The only info about ncs in mr_rosetta I have been able to find online pertains to extracting NCS from search models or mr_rosetta assembled models. Thanks, Stefan ------------------------------------------------------------------------------------------------------- Stefan D. Knight, PhD Professor of Biology Department of Cell and Molecular Biology, Uppsala University Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala Sweden Voice: +46 (0)18 471 45 54 Fax: +46 (0)18 53 03 96 E-mail: stefan(a)xray.bmc.uu.se ------------------------------------------------------------------------------------------------------- "We trained very hard, but it seemed that every time we were beginning to form into teams, we would be reorganised. I was to learn later in life that we tend to meet any new situation by reorganising - and a wonderful method it can be for creating the illusion of progress while producing confusion, inefficiency and demoralisation." – Gaius Petronius Arbiter (d. AD 66) -------------------------------------------------------------------------------------------------------

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fem command/memory error
by Matteo Colombo 14 May '14

14 May '14

Hi Pavel, I downloaded the last released version of phenix (phenix-1.9-1692) and I would like to run the "feature enhanced map" command. However, when I run it I got the following Memory Error that I didn't have in the previous version of phenix. r_work: 0.1867 r_free: 0.2372 Max B subtracted from atoms and used to sharpen map: 20.0 b_sharp: 25.0 FEM loop: done so far: 10%Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 120, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6/../../cctbx_project/mmtbx/command_line/development_fem.py", line 99, in run sharp=params.sharp, signal_threshold=params.signal_threshold) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 112, in __init__ progress_counter = progress_counter) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 204, in fem_loop weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 276, in fem_loop_ weighted_average_manager = weighted_average_manager) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 234, in one_iteration m = get_map(mc=mc_wa, cg=crystal_gridding) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/maps/fem.py", line 20, in get_map fourier_coefficients = mc) File "/usr/local/phenix-1.9-1692/cctbx_project/cctbx/miller/__init__.py", line 4357, in __init__ conjugate_flag=True) MemoryError My OS is Ubuntu precise 12.04 LTS, system 32 bit Thanks in advance Matteo -- Matteo Colombo PhD Groupe Extremophile et grands assemblages moléculaire Institut de Biologie Structural J. P. Ebel 6, rue Jules Horowitz F-38027 GRENOBLE Cedex 1

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Re: [phenixbb] Non bonded contacts
by Mark A Saper 14 May '14

14 May '14

Pavel, Your suggestion of setting the alt-loc the same for the two residues in order to avoid the non-bonded contact restraint is not working yet. Do the residues need to be in the same chain Thanks, Mark On May 12, 2014, at 12:23 PM, Mark A Saper <saper(a)umich.edu> wrote: > Hi Pavel, > > I'll try that. I have a PLP cofactor and a lysine. I refined with them forming a Schiff base but the maps had large delta F indicating that the PLP ring was being pulled out of density. So now I am modeling it as PLP and Lys. But there is some bridging density. I want to see how close the Lys would extend if it didn't see the PLP. > > Thanks, > Mark > > On May 9, 2014, at 8:25 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > >> Hi Mark, >> >>> Is there a straightforward way to turn off non-bonded restraints between 2 residues? I see the restraints in the .geo file. Thanks. >> >> you can asigne them diferent altloc identifiers and then they will not see each other via non-bonded interactions. >> If these two residues in question are symmetry mates then there is a keyword for this: custom_nonbonded_symmetry_exclusions . >> >> Also, I wonder why you want to do this? >> >> Pavel >> >

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Using command-line Phenix from the Mac graphical installer
by Nathaniel Echols 13 May '14

13 May '14

A public service announcement: the graphical installer gives you access to all of the same tools as the command-line installer. The only differences are a) the location, and b) we remove some of the bulkier data files that are not required for normal operation. (Which means that the graphical installation is actually about 300MB smaller.) Instructions are here: https://www.phenix-online.org/version_docs/1.9-1692/install-setup-run.html#… In general, I recommend that all (64-bit) Mac users run the graphical installer unless you absolutely need Phenix to go somewhere other than /Applications. (I know that some of you are already aware of this, but I've had to make this same suggestion twice already today, and the command-line installer is more work to support, thank you Apple.) -Nat

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Phenix version 1.9 released
by Paul Adams 13 May '14

13 May '14

The Phenix developers are pleased to announce that version 1.9 of Phenix is now available. Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights from this version: Significant changes to the content and presentation of documentation, major improvements to HySS and AutoSol for SAD phasing in cases of weak signal, new Phenix/Rosetta refinement program for difficult low resolution refinements, new real space refinement program for refinement against a density map (e.g. cryo-EM), feature enhanced maps (FEM) enhance weak features and reduce noise and bias, new composite omit map program, unified MolProbity validation program (consistent with the MolProbity web server), proximity restraints for group displacement parameter refinement in phenix refine, and option for automated chemical linking in phenix.refine. Graphical interface: ==================== - Rearranged main interface to accompany documentation changes - New Phenix releases may be downloaded directly from the GUI (requires previously registered academic email address or permanent user credentials) - Added command to remove large data files (.geo, .kin, .ccp4, etc.) from a project directory to conserve disk space - Changes to support Mac OS 10.9 ("Mavericks") General: ======== - Re-organized and updated documentation - Binary installers for Ubuntu (10.04 or later) available - Python built as shared library in Linux builds (facilitates Rosetta hybrid) - new commands: phenix.composite_omit_map, phenix.rosetta_refine, phenix.molprobity, phenix.sceds, phenix.fem, phenix.real_space_refine, and many smaller utilities Refinement: =========== - phenix.refine: - similarity restraints for group isotropic B-factor refinement - set by group_b_iso.use_restraints (default=True) - data/restraints targets weight is determined automatically; can be adjusted by setting group_b_iso.restraints_weight (larger value makes restraints stronger) - various rotamer handling bug fixes - Automatic linking generation in phenix.refine and other programs that require restraints can be requested using the parameters link_all=True - handles any appropriate ligand-protein or ligand-nucleic acid covalent bonds, including sugars, amino acid modifications, and other prosthetic groups - behavior can be adjusted by setting maximum bond distances parameters - added "bfactor" and "occupancy" keywords to atom selection syntax (also applies to phenix.pdbtools) - Integration with DivCon suite (http://www.quantumbioinc.com) for QM refinement of ligands (requires separate license and installation) - phenix.rosetta_refine (new command): - Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures for difficult cases at low resolution - reference: DiMaio et al. (2013) Nature Methods - phenix.ensemble_refinement: - enabled use of experimental phases (MLHL target) - phenix.real_space_refine (new command): - tool to refine a model against a map (especially EM maps) - phenix.morph_model: - fixed serious bug present in versions 1449-1626 that resulted in incorrect offset being applied Experimental Phasing and Model Building: ======================================== - HySS (phenix.hyss): - Substructure search much more fully automated: - Search first with Patterson seeds and direct method - If no clear solution, try more seeds, Phaser completion, and varying resolution - Full parallelization makes the search rapid - AutoSol: - Now much more powerful for weak SAD data: - Incorporates new automated Hyss search - Classic solvent flipping density modification after Resolve density modification - Tests several values of smoothing radius for solvent boundary identifcation for weak data - Iterates heavy-atom substructure search with Phaser completion including density after density modification and using model after model-building - Require solutions scored by correlation to be substantially better than altermatives before eliminating alternatives - Building with helices_strands_only set as default for data at lower than 3 Angstroms - AutoSol, AutoBuild, and LigandFit: - You can now specify the value of the test set flag for the free data with test_flag_value=xxxx Molecular Replacement: ====================== - phenix.sceds (new command, formerly phaser.splitter): - implements normal mode-based domain finding method - reference: McCoy et al. (2013) Acta Cryst D69 - phenix.find_alt_orig_sym_mate: - offset the produced MLAD value with log(0.9) to avoid negative values if identical structures were to be compared. Consequently older versions therefore yield MLAD values which are 0.10536 smaller than the current version. New commands: ============= - phenix.rosetta_refine (new command): - Hybrid Rosetta/Phenix refinement of protein X-ray crystal structures for difficult cases at low resolution - reference: DiMaio et al. (2013) Nature Methods - phenix.molprobity (new command): - Unified validation tool for command-line users; similar to existing comprehensive validation in the Phenix GUI - optional output of script for viewing results in Coot, or kinemage file - phenix.composite_omit_map (new command): - Default method uses very fast iterative de-biasing procedure - Can also generate either a simple or composite omit map with refinement and optional simulated annealing - Will generate multiple map types at once - parallelizable on multi-core systems or managed clusters - phenix.sceds (new command, formerly phaser.splitter): - implements normal mode-based domain finding method - reference: McCoy et al. (2013) Acta Cryst D69 - phenix.real_space_refine (new command): - tool to refine a model against a map (especially EM maps) - phenix.fem (new command): - Compute "feature-enhanced" map ("FEM") - this protocol modifies a 2mFo-DFc sigmaA-weighted map such that the resulting map has strengthened weak signal, if present, and a reduced amount of noise and model bias. - combines randomization and averaging, treatment of missing reflections, residual composite omit map, and histogram equalization - resulting maps are more interpretable and have less bias compared to the starting 2mFo-DFc map - very fast procedure, no refinement required - phenix.map_to_structure_factors (new command): - convert map into structure factors (also intended for EM) - phenix.angle (new command): - compute angle between two axes or two atom selections - phenix.model_model_distances (new command): - Given two PDB files compute distances per atom, residue, chain, model and overall. It is assumed (and asserted in the code!) that the amount and order of atoms in both files are identical. - phenix.fab_elbow_angle (new command): - Calculating Fragment Antigen-Binding (Fab) elbow angle - phenix.f000 (new command): - Given PDB file estimate F(0,0,0); includes atomic model and bulk-solvent Ligands: ======== - phenix.ligand_identification: - Now you can use ligand cif files (in addition to .pdb files) to build your own custom ligand library. Just specify "Ligand directory" (GUI) or use keyword "ligand_dir" (command line) to tell the program to use .pdb or .cif files in your own ligand directory. - Bug fix to properly handle mtz labels when using difference maps. For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Re: [phenixbb] HLs not recognised
by Nathaniel Echols 13 May '14

13 May '14

Here is the problem: phenix.mtz.dump resolve_1_190_phenix.mtz ... HLA xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) HLB xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) HLC xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) HLD xxxxx 100.00% 0.00 0.00 A: phase probability coefficients (Hendrickson/Lattman) We ignore arrays with all zeros, since they're obviously not correct - however, the feedback given to the user is deficient. I am open to suggestions about how we can improve this, but I am reluctant to assault users with pop-ups every time bogus information is detected, especially since this will increase the latency of the GUI. The file from AutoSol you should actually use is probably named overall_best_refine_data.mtz, which contains the original, purely experimental phases (along with data and R-free flags, of course). We don't recommend using the density-modified phases as restraints. (I am not sure why Resolve would output all zeros; that is a question for Tom. I did however notice the same thing in a file generated by AutoSol for a tutorial dataset.) -Nat On Mon, May 12, 2014 at 8:21 AM, Jonathan Grimes <jonathan(a)strubi.ox.ac.uk>wrote: > > hi nat > > i created this mtz file.....by taking a resolve.mtz > and putting it back thru phenix. > > from the GUI and from the command line phenix > doesnt like my HLs coeffs. > > thanks > jon > > Dr. Jonathan M. Grimes, > NDM Senior Reseach Fellow Diamond Research > Fellow > University Research Lecturer Diamond Light > Source > Division of Structural Biology Diamond House > Wellcome Trust Centre for Human Genetics Harwell Science Campus > University of Oxford Didcot > Roosevelt Drive, OX11 0DE > Oxford OX3 7BN, UK > > Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk > Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 > > > > ---- Original message ---- > >Date: Mon, 12 May 2014 07:44:14 -0700 > >From: Nathaniel Echols <nechols(a)lbl.gov> > >Subject: Re: [phenixbb] HLs not recognised > >To: Jonathan Grimes <jonathan(a)strubi.ox.ac.uk> > >Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> > > > > This is a little strange - the GUI should not be > > allowing you to select an array that won't work for > > refinement. Could you please send me (off-list!) > > both MTZ files that you tried using? (I don't > > think I need data or anything else for this.) > > thanks, > > Nat > > > > On Mon, May 12, 2014 at 5:49 AM, Jonathan Grimes > > <jonathan(a)strubi.ox.ac.uk> wrote: > > > > i have now used phenix to read in the mtz file, > > read all the arrays > > and make a new mtz file. > > > > phenix recognised the HLs as Hend/latt coeffs. > > > > i used the eff file to run phenix.refine at the > > command line > > and got this error > > > > Not a suitable array of experimental phases: > > refinement.input.experimental_phases.labels=HLA,HLB,HLC,HL > > > > The phases were orginally derived by Phenix > > using the auto solve GUI. > > Jon > > > > Dr. Jonathan M. Grimes, > > NDM Senior Reseach Fellow > > Diamond Research Fellow > > University Research Lecturer > > Diamond Light Source > > Division of Structural Biology > > Diamond House > > Wellcome Trust Centre for Human Genetics > > Harwell Science Campus > > University of Oxford > > Didcot > > Roosevelt Drive, > > OX11 0DE > > Oxford OX3 7BN, UK > > > > Email: Jonathan(a)strubi.ox.ac.uk, Web: > > www.strubi.ox.ac.uk > > Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - > > 287547 > > > > ---- Original message ---- > > >Date: Mon, 12 May 2014 11:32:39 +0100 > > >From: phenixbb-bounces(a)phenix-online.org (on > > behalf of Jonathan Grimes > > <jonathan(a)strubi.ox.ac.uk>) > > >Subject: [phenixbb] HLs not recognised > > >To: phenixbb(a)phenix-online.org > > > > > > > > > I am trying to refine a structure at low > > resolution and would like to > > > use phase restraints. using the GUI even > > though HLs are present > > > in the MTZ file, and are type > > “A”…checked with CAD…..i am not given > > > the option of selecting them. > > > > > > not clear to me what I’m doing wrong. > > > > > > hints most wellcome > > > thanks > > > jon > > > > > > > > >Dr. Jonathan M. Grimes, > > >NDM Senior Reseach Fellow > > >University Research Lecturer > > >DIAMOND Research Fellow > > > > > >Division of Structural Biology > > >Wellcome Trust Centre for Human Genetics > > >University of Oxford > > >Roosevelt Drive, > > >Oxford OX3 7BN, UK > > > > > >Email: Jonathan(a)strubi.ox.ac.uk, Web: > > www.strubi.ox.ac.uk > > >Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - > > 287547 > > > > > >_______________________________________________ > > >phenixbb mailing list > > >phenixbb(a)phenix-online.org > > >http://phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb >

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gui occupancy group selection crash
by Petri Kursula 12 May '14

12 May '14

Hi, I’m trying to set up constrained occupancy groups in the GUI, but trying to add selections, the entire Phenix GUI crashes. This happens when clicking the plus sign in the dialogue attached. This is with the PHENIX-1.9-1692 build (updating from 1.8.x did not help) with OSX Mavericks (10.9.2). I know this worked before smoothly, so there perhaps is a bug somewhere. Petri --- Petri Kursula, PhD project leader, adjunct professor Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland Department of Chemistry, University of Hamburg/DESY, Germany www.biochem.oulu.fi/kursula<http://www.biochem.oulu.fi/kursula> www.desy.de/~petri/research<http://www.desy.de/~petri/research> petri.kursula(a)oulu.fi<mailto:[email protected]> — [cid:9BE629E3-4781-4E71-BC21-2DB1CB2B9F59@localdomain]

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Continue mr_rosetta after system crash?
by Oliver Clarke 12 May '14

12 May '14

Hi all, I was running a mr_rosetta job on an 8-core machine, and after 3 days of apparently fruitful computation (784/1000 initial models generated), my system crashed for an apparently unrelated reason (there are no errors in the rosetta logs - I suspect a brief power outage or something of the sort). I am guessing the answer is no, but I just thought I’d check whether anyone knows of a way to continue such a job from where it left off without having to start from scratch? Best, Oliver.

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HLs not recognised
by Jonathan Grimes 12 May '14

12 May '14

I am trying to refine a structure at low resolution and would like to use phase restraints. using the GUI even though HLs are present in the MTZ file, and are type “A”…checked with CAD…..i am not given the option of selecting them. not clear to me what I’m doing wrong. hints most wellcome thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer DIAMOND Research Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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No bonded contacts
by Mark Saper 09 May '14

09 May '14

Is there a straightforward way to turn off non-bonded restraints between 2 residues? I see the restraints in the .geo file. Thanks. Mark

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Rosetta_refine stuck...?
by Jan Gebauer 09 May '14

09 May '14

Hello everyone, First of all thanks to the developers for improving the installation of rosetta_refine. In contrast to my experiences half a year ago, this time the installation was easy and straightforward. However, refining a 600 Aa @ 3.5 A with 4 mol per asu one more than one processor still completely breaks my computer. (Intel i5 2500K / 7.8 GB RAM) I think this might be a memory issue. Having only a "normal" PC, one process already uses 5GB of RAM which equals 60% of my RAM. With only one process running the first of five model was finished in roughly 3 hours. However, the second model already takes more than 10 hours, and the log file on the _ros_tempXXX file wasn't update for the last 9 hours. I can't see any progress, however it still uses 100% of one processor. Unix's top tells me that "reduce" is completely using this resource and that it had run for the last 821 minutes... so I guess rosetta_refine is somehow stuck? Any ideas why it is stuck and how to solve that? With kind regards, Jan Gebauer By the way: Is rosetta_refine meant to work on a "normal" Computer - like mine. In principle I would have access to a cluster, but set-up time there would be considerably long for me... -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

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FEM mtz won't open in coot
by de Waal, Parker 09 May '14

09 May '14

Hello Everyone, I'm having trouble opening the map file generated by phenix.fem in coot. Each time I try and load the .mtz file the follow error occurs 'Failed to find any suitable F/phi columns in the MTZ file'. Dumping the mtz file I can see: Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE 0 33 0 100.00 12.1 12.1 114.15 3.31 H H 2 NONE 0 33 0 100.00 12.8 12.8 114.15 3.31 H K 3 NONE 0 137 0 100.00 51.4 51.4 114.15 3.31 H L 4 NONE 0.0 10551.1 22963 71.24 406.13 406.13 39.60 3.31 F 2mFoDFc 5 NONE -180.0 180.0 22963 71.24 0.98 89.81 39.60 3.31 P PHI2mFoDFc 6 NONE 5.2 51589.8 0 100.00 1602.72 1602.72 114.15 3.31 F FEM 7 NONE -180.0 180.0 0 100.00 0.32 89.74 114.15 3.31 P PHIFEM If someone could help me to rename these columns to a coot friendly format so that I would be greatly appreciative. Best, Parker

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PHENIX.apply_ncs question
by Sun Bingfa 07 May '14

07 May '14

Hi guys, I've been working on a structure using NCS. When I run the phenix.apply_ncs to generate the whole structure using the original one chain PDB, it gave me a PDB with same atom number on the other chain. For example, I start with chain A and end in chain A and B (B is generated by NCS), while the atom number on chain B is just a duplicate of chain A, starting from 1. This cause error in the subsequent refinement trials. I'm wondering what program can correct this issue. Thanks, Bingfa

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PHENIX-Coot problem
by Marcelo Carlos Sousa 07 May '14

07 May '14

I recently updated to CCP4 6.4 including Coot. I updated the path in phenix to point to the coot wrapper startup script. Phenix then correctly starts Coot and both programs are "connected". However regularizations or real space refinement fail with the "Failed to find restraints for: …" message as if the dictionaries are not loading. This does not happen when starting Coot from the terminal or form CCP4i… Any ideas on how to solve this problem? ____________________________________________ Marcelo C. Sousa, Ph.D. Associate Professor Department of Chemistry and Biochemistry University of Colorado at Boulder 596 UCB Boulder, CO 80309 Phone: (303) 735 4341 Fax: (303) 492 8425

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Making beautiful crystallographic maps with FEM (Feature Enhanced Map) - new Phenix tool
by Pavel Afonine 07 May '14

07 May '14

Dear Phenix users, this is a quick announcement of a new Phenix tool to improve crystallographic maps. Link below provides most information: from method overview and examples to usage details: http://www.phenix-online.org/presentations/fem_06MAY2014.pdf Should you have any questions, bug reports or any other feedback *please send it to me directly*. All the best, Pavel

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LAST DAY TO REGISTER: SBGrid/NE-CAT Computing School
by Michelle Ottaviano 07 May '14

07 May '14

We're in the final stages of planning for our June Computing School and *registration will close on Friday. *Join us in June for our data processing workshop followed by Phenix and Schrodinger/BioLuminate workshops. *Register Here <http://www.events.harvard.edu/profile/web/index.cfm?PKWebId=0x12902a67d>: Deadline Friday, May 9th* *Quo Vadis Structural Biology 2014* SBGrid/NE-CAT Computing School June 5-7, 2014 Harvard Medical School -- Boston, MA *Data Processing in Crystallography - June 5-6:* Speakers: Kay Diederichs, Phil Evans, Zbyszek Otwinowski, Jim Pflugrath, Dominika Borek, Piotr Sliz, Matt Benning, , Frank Murphy, David Neau, K. Rajashankar, Nick Sauter, Jon Schuermann, Clemens Schulze-Briese *Advances in Structure Determination with Phenix - June 7:* Paul Adams & Nathaniel Echols, Lawrence Berkeley National Laboratory Tom Terwilliger, Los Alamos National Laboratory *Improved Structural Modeling Using BioLuminate - June 7: * Melissa Landon, Ph.D., Schrodinger, Inc. Complete meeting details can be found here: https://sbgrid.org/news/sbgridne-cat-computing-school

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Occupancy refinement troubles
by Kieft, Jeffrey 07 May '14

07 May '14

Hello All, Question about occupancy refinement. I'm refining an RNA structure at 2.0 Angstrom resolution with bound ligands iridium hexammine and spermine. The location of the former can be confirmed in an anomalous difference map, but they are likely not full occupancy...likewise the spermine is likely less than one. When I use occupancy refinement, it leaves the RNA at full occupancy as expected, but refines each atom of the irhex and spermine individually, in some cases driving the occupancy to 0 for some atoms. It seems like this was an issue in the past, but I'm still seeing it. Any ideas? Could if be that Phenix doesn't recognize those ligands? Parameter files wrong? Thanks for help! Jeff

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Current version download
by Marcelo Carlos Sousa 06 May '14

06 May '14

I was checking for the current official Phenix release and the website lists 1.9-16090. However, upon downloading it seems to be 1.8.4-1496… Am I doing something silly? Marcelo

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Geometry regularization in phenix.pdbtools
by Francis Reyes 06 May '14

06 May '14

Hi all, I always enjoyed geometry regularization in phenix.pdbtools. Has it been moved elsewhere? phenix.pdbtools file.pdb --geometry-regularization ceases to exist . Thanks, F

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