- phenixbb - phenix-online.org

molecular replacement keeping hetatms?
by Murpholino Peligro 27 May '14

27 May '14

Can I do molecular replacement with phenix/phaser, keeping all the waters from the first model from the first data set? >From here ( http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#WATER), I should change all the HOH labels to something like WWW. Then I guess that I should put HOH labels again in the solution model, for the following refinement in phenix.refine. Is that it?... Any suggestions? thanks again!

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(no subject)
by Fulvio Saccoccia 27 May '14

27 May '14

Dear phenix users and developers, in the past I usually used the fix_rotamers=true options to fix some residue issues. Now, this option is lacking (I currently use the dev-1702 version of phenix) but I was wondering if some other option does replace it. In addition, I would like to know better how real_space_refinement works; is there any tutorial or presentation about it? Thanks in advance -- Fulvio Saccoccia, PhD Dept. of Biochemical Sciences Sapienza University of Rome 00185, Rome (Italy) Phone: +39 06 4991 0556 https://www.researchgate.net/profile/Fulvio_Saccoccia/?ev=hdr_xprf

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Workshop announcement @ Inst Pasteur Montevideo - Uruguay : Modern Approaches in Drug Discovery for Neglected Infectious Diseases
by Alejandro Buschiazzo 23 May '14

23 May '14

Dear Colleagues: We are pleased to announce the Workshop: "Modern Approaches in Drug Discovery for Neglected Infectious Diseases" at the Institut Pasteur de Montevideo (Uruguay). *Dates:* November 3rd - 8th, 2014 *Venue**: *Institut Pasteur de Montevideo (Montevideo, Uruguay) *Invited speakers:* Wim Hol (University of Washington, Seattle, USA), Paul Michels (University of Edinburgh, Edinburgh, UK), Celerino Abad-Zapatero (University of Illinois at Chicago, Chicago, USA), Hugo Cerecetto (UdelaR), Marcelo Comini (IP Montevideo), Sergio Pantano (IP Montevideo), Alejandro Buschiazzo (IP Montevideo)* * *Aim:* The general aim of this International Workshop is to train students in state-of-the-art approaches for drug discovery and rational design, with special emphasis on target-based methods. The course will provide with a multidisciplinary view, with invited professors covering a diverse set of subjects : protein crystallography, in silico methods for molecular simulations, medicinal chemistry and biology of neglected infectious diseases.** For details of the activity please see the preliminary program. <http://www.pasteur.edu.uy/images/program_v.5-5-14.2.pdf> The course will be in English. This activity is supported by the /Center for Structural Biology of the MERCOSUR /(CeBEM <http://www.cebem.org.ar/>), jointly with the /United Nations University Biotechnology Programme for Latin America and the Caribbean/ (UNU - BIOLAC <http://unu.edu/about/unu-system/biolac>). * **Applicants:* Graduate students and young research scientists are encouraged to apply. 24 students will be selected among the applications. The Course will provide financial support for the students, covering registration fees, and for the case of those coming from abroad, all local expenses (lodging, per diem and local transportation). /* The application deadline is September 8th, 2014. The results will be announced by September 30th.*/ The application form, activity program, contact information and other details can be found at the web site of the course <http://www.pasteur.edu.uy/index.php/en/teaching/courses/54-ensenanza/cursos…> Please address further inquiries toSBDD_course(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Three positions open at the MAX IV Laboratory
by Marjolein Thunnissen 23 May '14

23 May '14

The MAX IV facility, the largest and most ambitious Swedish investment in research infrastructure, will be the brightest source of x-rays worldwide and will replace the existing laboratory, which today consists of the storage rings MAX I, II and III. The new MAX IV facility will become operational in June 2016. To extend the suite of already funded beamlines, MAX IV Laboratory is planning the next set of beam lines. Therefore The MAX IV laboratory in Lund has opened two positions within the life-science division. We are looking for two beamline scientists, one for the biomedical imaging beamline MEDMAX and one for the microfocus beamline MicroMAX. For both these positions the scientist will be overseeing the development, construction and commissioning of the MedMAX, respectively MicroMAX beamline from its conceptual stage to full operation. Both beam lines are planned to be cutting edge beam lines, fully exploiting the excellent properties of the MAX IV 3GeV storage ring. In addition we are also looking for a software engineer to be engaged in the design of the MX software infrastructure at the beamline for protein crystallography which is under construction, BioMAX. More information on these positions can be found at https://www.maxlab.lu.se/positions and the links within this page, or from our Life-Sciences director Tomas Lundqvist . best regards Marjolein Thunnissen [cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC] Marjolein Thunnissen Science Coordinator MX MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/>

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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 16 May '14

16 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 >

4 4

gui occupancy group selection crash
by Petri Kursula 13 May '14

13 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]

2 1

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.

2 1

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

2 2

No bonded contacts
by Mark Saper 10 May '14

10 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

2 1

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/

2 1

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

5 7

PHENIX.apply_ncs question
by Sun Bingfa 08 May '14

08 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

2 2

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

2 3

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

1 0

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

1 0

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

2 1

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

2 1

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

2 1

Phenix-rosetta refinement problems
by Oliver Clarke 05 May '14

05 May '14

Hi all, I am struggling a little to get Rosetta and phenix to play happily with one another (I’d like to use the phenix.rosetta_refine module). I am currently using the latest nightlies of phenix (1.9-1690) and rosetta (2014.16.56682), and I run into errors (reproduced below) when attempting to build the phenix-rosetta interface. Does anyone have any insights as to how to fix this problem, or suggestions as to which pair of phenix and rosetta versions are known to be compatible with one another? Many thanks, Oliver. Errors while building phenix-rosetta interface: <snip> chdir(tempdir_.c_str()); src/core/scoring/cryst/PhenixInterface.cc:375:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::string)': src/core/scoring/cryst/PhenixInterface.cc:949:25: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1075:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'std::string core::scoring::cryst::PhenixInterface::calculateDensityMap(core::pose::Pose&, bool)': src/core/scoring/cryst/PhenixInterface.cc:1095:25: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1104:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ g++ -o build/src/release/linux/3.11/64/x86/gcc/4.8/python/core/scoring/MinimizationGraph.os -c -std=c++98 -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -pipe -ffor-scope -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/MinimizationGraph.cc cc1plus: all warnings being treated as errors scons: *** [build/src/release/linux/3.11/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors.

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Post Doctoral Positions in Membrane Protein Structure and Function at the National Institutes of Health (NIH)
by Anirban Banerjee 03 May '14

03 May '14

Dear all, Please circulate to those who may be interested - The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We will combine structural techniques such as macromolecular crystallography with biophysical and biochemical methods such as reconstitution based biochemistry, electrophysiology together with synthetic chemistry to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH. The DC Metro area is a wonderful place to live, the weather is pleasant and is a vibrant international community. In terms of scientific opportunities, the NIH is absolutely unique in bringing scientists from a virtually all corner of biomedical sciences in one campus. The Cell Biology and Metabolism program is part of the National Institute of Child Health and Human Development (NICHD). Our lab also has an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). The candidates should hold a Ph. D. degree, must be motivated and a have strong background in biochemistry or structural biology. Experience with protein expression, purification and biochemical characterization is required. Prior experience in membrane protein biochemistry or insect/mammalian expression systems will be added advantages. Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests. Disclaimers: The NIH is dedicated to building a diverse community in its training and employment programs and this position is subject to a background investigation. Thanks very much. Best, Anirban

1 0

Partial Model for Mol Rep.
by Yuri 02 May '14

02 May '14

Hi Everyone, I am trying to solve a structure (to 2.15 Ang). I am pretty sure about one of the domains fold but it only covers residues 26-250 while the whole protein is 470aa. Could I attempt to use this small part of the protein to phase my data and hopefully start building? How is that handled in PHENIX? ps. Selenomet protein will be expressed soon.. -- Yuri Pompeu, Ph.D.

2 1

refining two chains into same density
by Scott Horowitz 02 May '14

02 May '14

I have a strange case where I think there are two separate protein chains that are partially occupying the same spot (i.e. two proteins:one binding site=half of each bound). I'd really like to try to simultaneously refine both chains at partial occupancy into this density, but when I tried this (not surprisingly) it terminated because there were some overlapping atomic coordinates between the two chains. Is there a way to work around this? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

2 1

phenix start-up error !
by abhisek Mondal 01 May '14

01 May '14

hi. I have recently installed phenix-1.8.4 in my lab's RHEL work-station using './install' command. When i try to use 'phenix command' , the cursor of the terminal goes on blinking for almost hours, before opening the gui. Is there any way to avoid such long start-up time.! thank you. -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics* *Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*

2 3

problem with MR
by Subhani Bandara 30 Apr '14

30 Apr '14

Hi all, I am trying to solve the structure of 7 KDa protein with a cubic space group at 1.35A resolution with Phaser-MR. It gives the error massage saying "The composition you have entered has a protein/nucleic acid content of 300.3%, which is impossible. Decrease your composition" and stops. This appears even if I give one chain as search model and say there is only one component copy. How can I fix this. Thanks Subhani

3 2

CASP 11: Call for targets to assess the state of the art in protein structure modeling
by Torsten Schwede 29 Apr '14

29 Apr '14

Summary: CASP is soliciting target proteins for structure prediction - specifically proteins with new folds, membrane proteins, disordered proteins, oligomers, complexes, and multi-domain proteins. Call for targets: ============= As many of you know, CASP (Critical Assessment of Structure Prediction) has been assessing the state of the art in modeling protein structure from sequence since 1994, running a community experiment once every two years. In these experiments, information on soon to be solved structures is collected from the experimental community, and the sequence data are passed to the structure modeling community so that blind predictions of structure can be collected and assessed (1). Over that period CASP has seen enormous progress in the quality of modeled structures (2), but many problems remain. CASP is only possible because of the generous participation of the experimental community in providing the modeling targets (3). The prediction season for the next full biannual experiment, CASP 11, begins May 1, and so we are now asking for your help in reaching our goal of releasing at least varied 100 targets in a the three-month period. We need all sorts of targets, spanning the categories below: 1. (More than ever) novel folds and membrane protein targets. Even with the extended collection season provided by CASP ROLL, there will be still a shortage. There are some interesting methods developments for ab initio modeling, and it is important to be able to decisively evaluate their effectiveness. 2. Oligomers, complexes, and multi-domain proteins: This round, CASP has entered collaboration with CAPRI for specifically assessing the accuracy of predictions of protein-interactions and relative domain orientation. 3. Targets containing significant amounts of disordered structure, so as to test the ability of methods to identify these regions. We are especially interested in targets where disorder has been directly characterized experimentally, e.g. by NMR. 4. A diversity of comparative modeling targets. Cases where there is fairly high sequence identity (30-50%) between the target structure and an available template are valuable for testing the degree to which model accuracy can approach that of experiment, particularly in functionally critical regions. Cases with lower sequence identity to template, right down to undetectable, are valuable for testing the ability of the methods to detect remote homologs, to overcome challenging alignment difficulties, to make use of multiple templates, and to build regions of the structure not obviously available from a template. 5. Some targets will also be used to test methods of structure refinement. In these cases, the best model received for a target will be released to the refinement community, who will subsequently submit new models. This too is an area where there have been some exciting developments in the last year, so we are hoping for significant progress. Refinement targets are selected based on the nature of the errors in the initial models. Because of the extended process, these targets need to be available for longer before release of the experimental structure. Procedure ========= For those of you who have not provided targets to CASP before, the procedure is simple. There are three ways to submit targets: (1) Go the target submission web page and fill in the easy form; (2) When you submit your co-ordinates to the PDB, tick the 'CASP HOLD' box, automatically setting up a target entry; (3) Send an email the prediction center with details. If you have queries, there is very experienced prediction center staff to deal with them. The key thing is timing: We need a window of at least four weeks between receiving information about a target and the release of your experimental structure. A longer window - up to eight weeks - is often useful, for example so that a target can be used to test refinement methods, but is not essential (note that using the PDB target submission route automatically selects eight weeks). We don't need your experimental structure in advance of its release by the PDB, provided that will happen by the end of August. Please consult the target submission page for more details: http://www.predictioncenter.org/casp11/targets_submission.cgi There are already many prediction teams signed for CASP 11, and so any targets provided will receive plenty of attention. If you have a suitable target now, we are ready to receive it. If new targets come up before mid of July, we would also love to have them. (After July, we will continue with CASP ROLL for novel folds, disordered proteins, and membrane proteins). So please get in touch whenever a suitable opportunity arises, and help improve modeling methods. Thanks, CASP organizing committee John Moult, IBBR, University of Maryland, USA Anna Tramontano, University of Rome, Italy Krzysztof Fidelis, University of California, Davis, USA Andriy Kryshtafovych, University of California, Davis, USA Torsten Schwede, SIB & Biozentrum University of Basel, Switzerland References ========= 1. Moult, John; Fidelis, Krzysztof; Kryshtafovych, Andriy; Schwede, Torsten; Tramontano, Anna (2014). Critical assessment of methods of protein structure prediction (CASP) - round X. Proteins, 82(S2), 1-6. 2. Kryshtafovych A, Fidelis K, Moult J. (2014) CASP10 results compared to those of previous CASP experiments. Proteins. 82 (S2):164-174. 3. Kryshtafovych, Andriy; Moult, John; Bales, Patrick; Bazan, J Fernando; Biasini, Marco; Burgin, Alex; Chen, Chen; Cochran, Frank V; Craig, Timothy K; Das, Rhiju; Fass, Deborah; Garcia-Doval, Carmela; Herzberg, Osnat; Lorimer, Donald; Luecke, Hartmut; Ma, Xiaolei; Nelson, Daniel C; van Raaij, Mark J; Rohwer, Forest; Segall, Anca; Seguritan, Victor; Zeth, Kornelius; Schwede, Torsten (2014). Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10(th) Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins, 82(S2), 26-42. Get in touch: casp(a)predictioncenter.org More information: http://www.predictioncenter.org/casp11/ Submit a target: http://www.predictioncenter.org/casp11/targets_submission.cgi

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MRage problem
by Appu kumar 27 Apr '14

27 Apr '14

Hello all, I am trying to find the molecular replacement for a protein of 75kDa at 6.1A, Space group is I422. MRage gave me a good solution once. But when i repeated the MRage with same parameters, it is not giving me the same solution and giving me wrong solution. Would you please help me in getting the solution which i got once. I have the information about the euler anglle. I will be highly grateful for the help. Thank you Appu

2 1

Low resolution refinement
by Appu kumar 26 Apr '14

26 Apr '14

Hello All, I want to refine the low resolution structure (6.5A). It is a membrane protein and we are able to phase it. It will be great help if any one can guide me how to proceed further with the refinement. People uses Phenix to refine low resolution structure, so phenix is really a good program to proceed for refinement against low resolution. Thank in advance Appu

3 2

Build Phenix from Source Code
by Chen Zhao 25 Apr '14

25 Apr '14

Dear all, I would like to try phenix.rosetta_refine and it is said in the online tutorial that the phenix should be built from source code in linux. However I ran into some errors, and I am too far from a linux export to figure it out. I am using Debian Wheezy with kernel 3.2.0-4-amd64. I download the source installer (phenix-installer-1.9-1683-source.tar) and run the installer as: # ./install --prefix=/usr/local/src --nproc=8 --no-gui (it seems from README-DEV that there is no --python-shared flag as described in the online tutorial) After while, I receive the following error message: ************************************************************************************************************************* Installing Imaging... log file is /workspace/setup/phenix-installer-1.9-1683/build-source/intel-linux-2.6-x86_64/cz-thinkpadw530-debian/tmp/Imaging_install_log getting package Imaging-1.1.7.tar.gz... using /workspace/setup/phenix-installer-1.9-1683/base/Imaging-1.1.7.tar.gz Traceback (most recent call last): File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install", line 9, in <module> install_cctbx_base.installer(args=sys.argv, log=sys.stdout) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 95, in __init__ self.build_cctbx_dependencies() File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 134, in build_cctbx_dependencies self.build_imaging() File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 349, in build_imaging confirm_import_module="Image") File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 325, in build_python_module_simple log=pkg_log) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", line 150, in call return call(args, log=log) File "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py", line 51, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/src/phenix-1.9-1683/build/intel-linux-2.6-x86_64/base/bin/python setup.py build ' failed with exit code 1 FATAL ERROR: aborting installation. ************************************************************************************************************************* I looked into Imaging_install_log, and at the end, I have the following errors: ************************************************************************************************************************* /usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libpython2.7.a: could not read symbols: Bad value collect2: error: ld returned 1 exit status error: command 'gcc' failed with exit status 1 *************************************************************************************************************************** Could anybody help me out? Thank you so much, Chen

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Re: [phenixbb] Build Phenix from Source Code
by Chen Zhao 25 Apr '14

25 Apr '14

I switched to version 1.8.4-1496 and this time the same error didn't occur. Also --python-shared/--with-rosetta flag works. But I ran it as # ./install --prefix=/usr/local/src --nproc=8 --no-gui --phython-shared then regenerate the dispatchers by running libtbx.refresh as shown in the message after installation. However, the installation is not complete, and if I source phenix_env.sh, the error message as below will show up: *************************************************************************************************************** bash: /usr/local/src/phenix-1.8.4-1496/bin/machine_type: No such file or directory bash: /usr/local/src/phenix-1.8.4-1496/bin/machine_version: No such file or directory bash: /usr/local/src/phenix-1.8.4-1496/bin/find-installation: No such file or directory *************************************************************************************************************** What else should I run to complete building phenix? PS. Because the first time I didn't append --python-shared flag, I build it again after deleting the original directory. I guess there might be files elsewhere that are changed, since I didn't have this error the first time. Thanks a lot, Chen On Thu, Apr 24, 2014 at 11:10 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: > OK, thank you for your suggestion! I will do that. But as a perfectionist, > I will try to finish with the installation. I later found that the flag is > --with-rosetta but not --python-shared... I have to build it again... > Crying... > > Best, > Chen > > > On Thu, Apr 24, 2014 at 11:06 PM, Meng, Wuyi <wuyi.meng(a)yale.edu> wrote: > >> Sbgrid version means the version compiled by sbgrid (on 130.132.25.142and other cbic Mac Pros). The Mac Pro runs 2x fast than csb and yale hpc >> computers of same phenix refinement, they have 8 cores too. Rosetta runs >> usually take days to weeks to finish, it is wise to do it on yale hpc >> cluster. >> >> Wuyi, >> >> On Apr 24, 2014, at 10:49 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: >> >> Dear Wuyi, >> >> Thank you for your warm help as always! But actually SBGrid is not >> "installed" in this machine (don't laugh, it is my laptop...) Do you mean >> phenix-1.8.4-1496 when saying the SBGrid version? I did try this version >> after you mentioned and at least it passed the step that gave me the error >> before. I will wait and see how the compilation goes. And if this works, >> hopefully there will be no error when running >> rosetta.build_phenix_interface. I will try the one on130.132.25.142 if >> nothing works. >> >> Thank you so much again! >> >> Good night, >> Chen >> <130.132.25.142> >> >> >> On Thu, Apr 24, 2014 at 10:35 PM, Meng, Wuyi <wuyi.meng(a)yale.edu> wrote: >> >>> phenix.rosetta_refine should work on 130.132.25.142 according to >>> following statement from sbgrid: >>> >>> Linux 64-bit We have installed and configured nightly versions >>> of Phenix and Rosetta to support the newly announced Phenix-Rosetta >>> refinement mentioned in Nature Methods. These experimental versions are not >>> the default, so you'll need to add version >>> overrides in your ~/.sbgrid.conf file: P HE N I X _ X = n i g h t l y R >>> O S E T T A _ X = n i g h t l y You can refresh your memory for setting >>> version overrides on our website. These new features are only available on >>> 64-bit Linux at this time. Phenix >>> generally has very good support for OS X, but Macs >>> seem to be a second tier platform for the Rosetta >>> developers. >>> >>> Wuyi, >>> >>> > On Apr 24, 2014, at 10:14 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: >>> > >>> > Dear all, >>> > >>> > I would like to try phenix.rosetta_refine and it is said in the online >>> tutorial that the phenix should be built from source code in linux. However >>> I ran into some errors, and I am too far from a linux export to figure it >>> out. I am using Debian Wheezy with kernel 3.2.0-4-amd64. I download the >>> source installer (phenix-installer-1.9-1683-source.tar) and run the >>> installer as: >>> > >>> > # ./install --prefix=/usr/local/src --nproc=8 --no-gui (it seems from >>> README-DEV that there is no --python-shared flag as described in the online >>> tutorial) >>> > >>> > After while, I receive the following error message: >>> > >>> > >>> ************************************************************************************************************************* >>> > Installing Imaging... >>> > log file is >>> /workspace/setup/phenix-installer-1.9-1683/build-source/intel-linux-2.6-x86_64/cz-thinkpadw530-debian/tmp/Imaging_install_log >>> > getting package Imaging-1.1.7.tar.gz... >>> > using >>> /workspace/setup/phenix-installer-1.9-1683/base/Imaging-1.1.7.tar.gz >>> > Traceback (most recent call last): >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install", >>> line 9, in <module> >>> > install_cctbx_base.installer(args=sys.argv, log=sys.stdout) >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 95, in __init__ >>> > self.build_cctbx_dependencies() >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 134, in build_cctbx_dependencies >>> > self.build_imaging() >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 349, in build_imaging >>> > confirm_import_module="Image") >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 325, in build_python_module_simple >>> > log=pkg_log) >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/install_cctbx_base.py", >>> line 150, in call >>> > return call(args, log=log) >>> > File >>> "/workspace/setup/phenix-installer-1.9-1683/lib/libtbx/auto_build/installer_utils.py", >>> line 51, in call >>> > raise RuntimeError("Call to '%s' failed with exit code %d" % >>> (args, rc)) >>> > RuntimeError: Call to >>> '/usr/local/src/phenix-1.9-1683/build/intel-linux-2.6-x86_64/base/bin/python >>> setup.py build ' failed with exit code 1 >>> > FATAL ERROR: aborting installation. >>> > >>> ************************************************************************************************************************* >>> > >>> > I looked into Imaging_install_log, and at the end, I have the >>> following errors: >>> > >>> > >>> ************************************************************************************************************************* >>> > /usr/bin/ld: /usr/local/lib/libpython2.7.a(abstract.o): relocation >>> R_X86_64_32S against `_Py_NotImplementedStruct' can not be used when making >>> a shared object; recompile with -fPIC >>> > /usr/local/lib/libpython2.7.a: could not read symbols: Bad value >>> > collect2: error: ld returned 1 exit status >>> > error: command 'gcc' failed with exit status 1 >>> > >>> *************************************************************************************************************************** >>> > >>> > Could anybody help me out? >>> > >>> > Thank you so much, >>> > Chen >>> > >>> > _______________________________________________ >>> > phenixbb mailing list >>> > phenixbb(a)phenix-online.org >>> > http://phenix-online.org/mailman/listinfo/phenixbb >>> > >>> > >>> > The information in this e-mail is intended only for the person to whom >>> it is >>> > addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> > contains patient information, please contact the Partners Compliance >>> HelpLine at >>> > http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error >>> > but does not contain patient information, please contact the sender >>> and properly >>> > dispose of the e-mail. >>> >> >> >

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HELP. semelno met refinement not working.
by Kenneth A. Satyshur 24 Apr '14

24 Apr '14

When I refine my seleno met residues in Phenix (1.8.4-1496) ALL my MSE are restrained to ONE conformer, in coot terms ptp #11 with a Chi 1 of 60 deg. This happens at the start of the second cycle when it does 'rsrl'. I can watch it happen in coot. POP! There is goes. Some of the MSE are in this conformation, but not all of them. This refinement is wrong, so how do I correct it? thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207

1 0

BCA/CCP4 Summer School in Protein Crystallography at Diamond
by Airlie McCoy 24 Apr '14

24 Apr '14

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 26th August to Sunday 31st August 2014. Applications close 1st May 2014. References are due by 8th May 2014. The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP4 programs will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines. For more information on eligibility, cost, and applications see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School.html Application form: http://extranet2.diamond.ac.uk/ISV/EventWidget/BCA/ApplicationsForm.aspx

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inputing tNCS into phenix?
by Yarrow Madrona 23 Apr '14

23 Apr '14

Hello, I recently posted a question about stalled R-factors and and obtained excellent help resulting in the realization that I have tNCS even though it is not picked up by X-triage. I know the transformation matrix of one molecule onto another but I am not sure how to input this into phenix (both the translation and the rotation) to improve refinement. Is there a way to do this? I'm sorry if this has already been covered. -Yarrow

2 5

Trouble Refining Ligand in Phenix
by Chris Fage 22 Apr '14

22 Apr '14

Hi Everyone, I am trying to refine a structure with a phosphorylated amino acid. After refining in Phenix, the Fo-Fc density (green) overlaps the 2Fo-Fc density for all atoms of the derivatized amino acid in Coot, almost as if I had not built in the residue. I am loading a .cif for the derivative when I run phenix.refine. I have also tried ReadySet, but when I click the "Run in phenix.refine" button, I see the message Error interpreting command line argument as parameter definition: "refine_65-coot-2.metal.edits" RuntimeError: Unexpected end of output. Am I just seeing noise, or is Phenix not actually refining this portion of the model? I would appreciate any suggestions. Best, Chris

2 2

Saenger class in nucleic acids
by Chen Zhao 22 Apr '14

22 Apr '14

Dear all, Could anybody point me to a reference for the saenger_class and leontis_westhof_class in nucleic acids? I just failed to find it in the long reference list in the phenix.refine online tutorial. Thanks a lot in advance, Chen

2 2

inputing tNCS into phenix?
by Yarrow Madrona 22 Apr '14

22 Apr '14

Hello, I recently posted a question about stalled R-factors and and obtained excellent help resulting in the realization that I have tNCS even though it is not picked up by X-triage. I know the transformation matrix of one molecule onto another but I am not sure how to input this into phenix (both the translation and the rotation) to improve refinement. Is there a way to do this? I'm sorry if this has already been covered. -Yarrow

1 0

Re: [phenixbb] Phenix composite omit map
by Chen Zhao 21 Apr '14

21 Apr '14

Dear all, Thank you all for your help and the program is running now. However, I met a AttributeError as " 'twin_model_manager' object has no attribute 'f_model_scaled_with_k1' ". Sorry for so many problems. Thank you so much, Chen On Mon, Apr 21, 2014 at 1:13 PM, Chen Zhao <c.zhao(a)yale.edu> wrote: > Dear Engin, > > Thank you so much for your reply! Yes, this is the problem because I am > using phenix-1.8.4-1496. I will download the newest version! > > Best, > Chen > > > On Mon, Apr 21, 2014 at 1:10 PM, Engin Özkan <eozkan(a)uchicago.edu> wrote: > >> Dear Chen, >> >> What version of Phenix are you using? phenix.composite_omit_map was >> recently added (post 1.8.4 release). Are you using a recent nightly >> (presumably dev-1579 as you suggest or even newer, like the release >> candidate for 1.9)? >> >> Engin >> >> >> On 4/21/14, 12:05 PM, Chen Zhao wrote: >> >> Thank you Tom, >> >> I understand what "command not found" mean, but I already sourced >> "phenix_env" in my bashrc. "phenix.list" works, also I have already run >> "phenix.autosol", "phenix.autobuild", "phenix.refine" without any problems. >> >> Thank you so much again! >> >> Sincerely, >> Chen >> >> >> On Mon, Apr 21, 2014 at 1:01 PM, Terwilliger, Thomas C < >> terwilliger(a)lanl.gov> wrote: >> >>> Hi Chen, >>> >>> "command not found" usually means the shell cannot find a particular >>> command. It often can be fixed by sourcing the right setup commands. >>> >>> If you type: >>> >>> phenix.list >>> >>> does it also say "command not found"? If so, you just need to source >>> the phenix version you want. When you install it phenix lists where this >>> directory is...If you are on a mac you will say something like this: >>> >>> >>> source /Applications/PHENIX-1.8.3-1479/Contents/phenix-1.8.3-1479/phenix_env >>> >>> and you can put that in your .cshrc file too (if you are using csh). >>> >>> Let me know if that doesn't do it! >>> All the best, >>> Tom T >>> >>> >>> >>> >>> On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote: >>> >>> Dear all, >>> >>> Hello! I am now running into a simple technical problem but I just >>> cannot figure it out. I am trying to create a composite omit map by phenix, >>> but when I typed in the command phenix.composite_omit_map XXX.eff based >>> on the instructions on >>> http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, >>> I got the error message "command not found". Could anybody help me out? >>> >>> Thank you so much in advance! >>> >>> Sincerely, >>> Chen >>> >>> >>> >> >> >> _______________________________________________ >> phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb >> >> >> -- >> Assistant Professor >> Dept of Biochemistry and Molecular Biology >> University of Chicago >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> >

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Berkeley Ligands workshop: registration deadline tomorrow
by Peter Zwart 21 Apr '14

21 Apr '14

Dear All, On May 2, 2014 the BCSB will be hosting a full day event dedicated to ligands in the life sciences. Access is free, but is limited to 30 participants. The lectures will be streamed allowing remote participation to this event. For onsite and remote attendance, please register to receive further instructions. The registration for on-site participation will be on a first come, first serve basis and will close tomorrow at noon. The program will cover structural science associated with ligands in the life sciences. Viewpoints from macromolecular crystallography, quantum chemistry, small molecule crystallography and solution scattering will provide the participants with a 360-degree perspective of the role of and technology associated with ligands in structural biology. Please have a look at https://sites.google.com/a/lbl.gov/ligands/home for more information. Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research 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 SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

1 0

Re: [phenixbb] Phenix composite omit map
by Terwilliger, Thomas C 21 Apr '14

21 Apr '14

Hi Chen, "command not found" usually means the shell cannot find a particular command. It often can be fixed by sourcing the right setup commands. If you type: phenix.list does it also say "command not found"? If so, you just need to source the phenix version you want. When you install it phenix lists where this directory is...If you are on a mac you will say something like this: source /Applications/PHENIX-1.8.3-1479/Contents/phenix-1.8.3-1479/phenix_env and you can put that in your .cshrc file too (if you are using csh). Let me know if that doesn't do it! All the best, Tom T On Apr 21, 2014, at 10:53 AM, Chen Zhao wrote: Dear all, Hello! I am now running into a simple technical problem but I just cannot figure it out. I am trying to create a composite omit map by phenix, but when I typed in the command phenix.composite_omit_map XXX.eff based on the instructions on http://www.phenix-online.org/version_docs/dev-1579/composite_omit_map.htm, I got the error message "command not found". Could anybody help me out? Thank you so much in advance! Sincerely, Chen

4 5

Re: [phenixbb] Stalled refinement
by Dale Tronrud 19 Apr '14

19 Apr '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, In P21 the equivalent positions are: xyz; -x,y+1/2,-z. In matrix form the operation to transform chain A onto the symmetry image of A is: Transform A -> Symmetry related A /-1 0 0\ /x\ / 0 \ | 0 1 0 | |y| + |1/2| \ 0 0 -1/ \z/ \ 0 / Now let's assume there are two molecules in the ASU related by a perfect two-fold, axis parallel to the crystal screw axis, but with arbitrary translations perpendicular. The equation to transform chain B onto A is: Transform B -> A /-1 0 0\ /x\ /t1\ | 0 1 0 | |y| + |0 | \ 0 0 -1/ \z/ \t3/ Now, the question is "What is the transformation that takes chain B directly onto the symmetry image of A?" We can derive that by transforming B onto A and then transforming that by the crystal screw axis. Transform B -> symmetry related A /-1 0 0\ //-1 0 0\ /x\ /t1\\ / 0 \ | 0 1 0 | || 0 1 0 | |y| + |0 || + |1/2| \ 0 0 -1/ \\ 0 0 -1/ \z/ \t3// \ 0 / Now simplify: / 1 0 0\ /x\ /-t1\ / 0 \ | 0 1 0 | |y| + | 0 | + |1/2| \ 0 0 1/ \z/ \-t3/ \ 0 / / 1 0 0\ /x\ /-t1\ | 0 1 0 | |y| + |1/2| \ 0 0 1/ \z/ \-t3/ What we get is an identity operator with a translation. Note, I didn't make any other assumptions. Whenever you have space group P21 and two-fold ncs with the same symmetry axis direction you will get pseudo-translation. With your crystal the ncs matrix is not aligned with the y axis all that well. I haven't calculated it exactly but it seems to be about 10 deg away. That must be enough to wipe out the Patterson peak and the pseudo-translation check in xtriage. As a side note, you mentioned that you didn't think this was pseudo-translation because the translation was not 0.5. A translation of 0.5 could lead to pseudo-centering which is a special case of pseudo-translation. If you had that your crystal would be nearly space group C2 and half your reflections would be systematically weak and this can cause problems with the free R. Dale Tronrud On 4/18/2014 2:16 PM, Yarrow Madrona wrote: > Hi Dale, > > You know a lot more (and probably have forgotten more) > crystallography theory than I will every know. But I thought that > rotational and translational NCS can be completely separate from > the space group symmetry. They can become confused when the NCS > operator is close to a crystallographic symmetry axis. I have P21 > symmetry between dimers but there is only one dimer in the unit > cell. They appear to have near perfect 2-fold symmetry between them > on the b-axis (according to the transformation matrix). However, > the translation between them is not close to 1/2 of a unit cell as > would be expected for a 2(1) screw axis. This makes sense because I > don't see a peak on the patterson map but I do see a peak on the > self rotation. X-triage also confirms the first part. > > I also get a translation of (0, 0.3, 0.3) but I thought this > wouldn't show up as translational "NCS" because it was not near > 0.5. I thought the difference between the vectors would not > perfectly superimpose to give a strong peak on a patterson map. > > Please correct me if I am wrong (because I probably am). It is > entirely possible I sound like an idiot. If so please let me know. > Otherwise I will never learn more about the fundamentals of > crystallography. If you have a good reference please let me know. > > -Yarrow > > > On Fri, Apr 18, 2014 at 9:34 AM, Dale Tronrud > <detBB(a)daletronrud.com <mailto:[email protected]>> wrote: > > Hi, > > I don't see how you can not have translational ncs. You are in > space group P21 and have an ncs two-fold parallel to y. Doesn't > this combination have to give rise to translational ncs? > > I may have screwed up my paper matrix multiplications but I come > up with a translational ncs of about (0, 0.3, 0.3) in fractional > coordinates. If the translation were 0.3333 you would only see > strong reflections for k+l=3n. This would result in a lot of weak > data and higher than expected free R's. > > Of course, xtriage should be screaming bloody murder and you > should be seeing the peak in the Patterson. I'm confused. > > Dale Tronrud > > On 4/17/2014 6:05 PM, Yarrow Madrona wrote: >> There is no significant peaks for translational NCS. I also >> didn't see anything in the patterson map. > >> However, the Multivariate Z score L-test gives 6.218. Also the >> observed Centric reflections are more intense than they should >> be but I don't suspect twinning in a monoclinic space group. > >> -Yarrow > > >> On Thu, Apr 17, 2014 at 4:37 PM, Paul Adams <pdadams(a)lbl.gov > <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> wrote: > > >> What does triage say about translation NCS? > > >> On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona >> <amadrona(a)uci.edu > <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> wrote: > >> Hello, > >> I using the latest stable build of phenx.refine (1.8.4) I >> recently collected data, processed and obtained an MR solution >> using phaser. I am stuck trying to refine with an Rfree sitting >> at 40% > >> I really want to know if the high Rfree is due to poor data >> quality or if non-crystallographic symmetry involving a near >> perfect two fold rotation between the two molecules in the ASU >> could somehow impede refinement. Stats and other information is >> below. Thank you for any help you can give. > >> -Yarrow > > >> Visually, the quality of the data is marginal at best >> (streaky/ice rings in many frames) despite good processing stats >> from XDS. Processing with mosflm or HKL2000 managed to index but >> failed pretty bad in integration and scaling. > >> Phaser gave high TFZ scores for 2 molecules in the asu (see >> below). > >> Density for a cholesterol like ligand shows up even though not >> present in the search model. > >> MolRep Self rotation shows rotational symmetry. > > https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf > > >> The 2 molecules in the ASU are related by almost a 2 fold >> rotation: > >> Rotation matrix for chain A to chain B: > >> new_ncs_group rota_matrix 1.0000 0.0000 0.0000 >> rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 >> 0.0000 1.0000 tran_orth 0.0000 0.0000 0.0000 > >> center_orth 15.2016 0.5245 33.7070 > >> rota_matrix -0.9860 -0.1636 -0.0309 rota_matrix -0.1659 >> 0.9511 0.2605 rota_matrix -0.0132 0.2620 -0.9650 >> tran_orth 34.3310 -24.0033 107.0457 > >> center_orth 15.7607 7.2426 77.7512 > >> RMSD, B onto A = 0.0007 after phaser RMSD, B onto A = 0.347 >> after one round of refinement in phenix > > >> Refinement using aniostropically corrected data (ucla web >> server: Services.mbi.ucla.edu/anisoscale > <http://Services.mbi.ucla.edu/anisoscale> >> <http://Services.mbi.ucla.edu/anisoscale>) did not improve the >> Rfree in refinement. > > >> Statistics are listed below: > >> UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21 > >> RESOLUTION NUMBER OF REFLECTIONS COMPLETENESS R-FACTOR >> R-FACTOR COMPARED I/SIGMA R-meas CC(1/2) Anomal SigAno >> Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed >> expected Corr > >> 5.99 8280 1927 2087 92.3% 3.1% 3.3% >> 8246 35.09 3.5% 99.8* 20* 0.909 1296 4.30 14606 >> 3401 3487 97.5% 3.3% 3.5% 14580 33.37 >> 3.8% 99.9* 11* 0.843 2273 3.53 17961 4244 >> 4445 95.5% 3.8% 3.9% 17944 31.11 4.4% 99.8* >> -2 0.789 2721 3.06 21954 5068 5221 97.1% >> 4.9% 5.1% 21933 24.81 5.6% 99.7* -2 0.780 3455 >> 2.74 25741 5830 5933 98.3% 7.6% 7.6% 25713 >> 18.88 8.6% 99.5* -2 0.782 4165 2.51 27859 >> 6311 6483 97.3% 10.8% 10.8% 27824 14.06 12.3% >> 99.1* -2 0.774 4385 2.32 31336 6979 7084 >> 98.5% 14.9% 15.3% 31296 10.49 16.8% 98.5* -4 >> 0.748 5095 2.17 32396 7347 7567 97.1% >> 22.3% 22.7% 32341 7.46 25.4% 97.3* -7 0.728 >> 5055 2.05 32254 7339 8047 91.2% 33.1% 33.5% >> 32075 5.06 37.5% 94.8* -6 0.724 5155 total >> 212387 48446 50354 96.2% 7.8% 7.9% 211952 >> 16.57 8.8% 99.7* -3 0.768 33600 > >> Processing with mosflm or HKL2000 managed to index but failed >> pretty bad in integration and scaling. > > >> Phaser: > >> SOLU SET RFZ=27.5 TFZ=24.2 PAK=0 LLG=1711 RF++ TFZ=64.6 PAK=0 >> LLG=3610 LLG=4865 > > >> _______________________________________________ phenixbb mailing >> list phenixbb(a)phenix-online.org >> <mailto:[email protected]> >> <mailto:[email protected] > <mailto:[email protected]>> >> http://phenix-online.org/mailman/listinfo/phenixbb > > > > >> -- 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 Tel: 1-510-486-4225 <tel:1-510-486-4225>, > Fax: 1-510-486-5909 <tel: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 > <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> ][ > 1-510-495-2506 <tel:%5B%201-510-495-2506> ] > > > > >> _______________________________________________ phenixbb mailing >> list phenixbb(a)phenix-online.org >> <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb > > _______________________________________________ phenixbb mailing > list phenixbb(a)phenix-online.org > <mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/phenixbb > > -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlNSKBMACgkQU5C0gGfAG12g4gCgqgM2umswKaUkxKYQFccDXeOc 3GgAoL5FjHVPUKyK+jkwLQ/BaVv15iiW =Phy4 -----END PGP SIGNATURE-----

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