- phenixbb - phenix-online.org

restraints between molecules in adjacent asymmetric units.
by jens j birktoft 04 Dec '14

04 Dec '14

Hi Everybody. Are there ways to restrain non-covalent interactions between molecules in adjacent asymmetric units? I know the custom bond procedure works well for covalent bonds. However I also would like to add restraints for (1) bond angles, (2) torsion angles (less important) and (3) nucleotide base-pairing. I know that all of these can be generated via the custom bond syntax, but that is a rather tedious and time-consuming process. Perhaps there is a simpler way I know this issue has been raised before but am unaware of any new developments. Cheers Jens -- +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft Director of Crystallography Structural DNA Nanotechnology Chemistry Department, New York University e-mail: jens.knold(a)gmail.com; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++++++++++++++++++++++++++++++++++++++++++++++++++

3 2

Intl Conf on Structural Genomics 2015: "Deep Sequencing Meets Structural Biology"
by Terwilliger, Thomas Charles 04 Dec '14

04 Dec '14

Dear Colleagues, We hope that you will be able to attend the International Conference on Structural Genomics 2015 "Deep Sequencing Meets Structural Biology", which will be held on the campus of the Weizmann Institute of Science in Rehovot, Israel June 7-11, 2015. This conference is intended to foster international collaboration and to provide an overview for the most recent developments in Structural Biology and Structural Genomics and future impacts on biology, medicine and disease. The scientific topics to be covered in ICSG 2015 include: · Deep sequencing for modeling and refinement of macromolecular structures · Membrane protein structure and function using complementary methods · Technological advances in XFEL, Cryo-EM, NMR, SAXS, MS, MX and macromolecular complexes · Combining low and high resolution data and modeling for structural biology · Synergistic use of 3D structures and deep sequencing to realize personalized medicine · Protein design and deep sequencing · Cancer, antibiotic resistance and drug discovery In order to widen the opportunities for younger researchers, we have organized satellite workshops before ICSG 2015 (during the day on June 7, 2015). These include: · Cryo-EM developments for structural biology [Sponsored by FEI] · PHENIX: Automated determination of molecular structures · HKL3000: From X-ray diffraction images to structure determination in minutes · Approaches to the translation of deep sequencing data into three-dimensions · Protein expression and characterization workshop · Proteopedia: A Scientific Wiki Bridging the Rift Between 3D Structure & Function You can see all the details of the conference at http://www.weizmann.ac.il/conferences/ICSG2015 . Five oral presentations will be chosen from the posters, and six poster prizes will be awarded, so be sure to submit your abstracts by April 15, 2015! Invited Speakers will include: Keynote Speakers: Shamil Sunyaev - Harvard Medical School Janet Thornton – EMBL/EBI - The FEBS National Lecturer Speakers: Arie Admon – Technion, Haifa Lucia Banci - CERM, University of Florence Pamela J. Bjorkman – CalTech, Pasadena Samir K. Brahmachari - CSIR-Institute of Genomics & Integrative Biology, Delhi Susan Buchanan - NIDDK, NIH, Bethesda Mark Gerstein - Yale University, New Haven Wayne Hendrickson - Columbia University Medical Center, New York Yvonne Jones - University of Oxford Luhua Lai - Peking University, Beijing Michael Levitt – Stanford University Michal Linial – The Hebrew University of Jerusalem Abraham Minsky - Weizmann Institute of Science, Rehovot John Moult - IBBR, University of Maryland, Rockville Nathan Nelson - Tel Aviv University Stefan Raunser - MPI of Molecular Physiology, Dortmund Monica Roth - Rutgers University, Piscataway Dinakar M. Salunke – Regional Centre for Biotechnology, Gurgaon Eran Segal - Weizmann Institute of Science Philip Selenko - Leibniz Institute of Molecular Pharmacology (FMP Berlin) Sachdev Sidhu - University of Toronto Rotem Sorek - Weizmann Institute of Science Jan Steyaert - VIB, Flanders, Brussels Dan Tawfik - Weizmann Institute of Science Gunnar von Heijne - Stockholm University Soichi Wakatsuki - Stanford University Shigeyuki Yokoyama - Genomic Sciences Center, RIKEN Yokohama Institute Ada Yonath - Weizmann Institute of Science Mingjie Zhang – Hong Kong University of Science & Technology We are looking forward to welcoming you to the Weizmann Institute in the June of 2015! Sincerely yours, ICSG 2015 Local Organizing Committee Joel L. Sussman, Gideon Schreiber, Tamar Unger and Israel Silman, Weizmann Institute ICSG 2015 International Organizing Committee Cheryl Arrowsmith, (Structural Genomics Consortium, Toronto) Lucia Banci, (University of Florence, Florence) Jacqui Beckmann, (Swiss Institute of Bioinformatics, Lausanne) Mark Gerstein, (Yale University, New Haven) Yvonne Jones, (University of Oxford, Oxford) Luhua Lai, (Peking University, Beijing) Katsumi Maenaka, (Hokkaido University, Sapporo) Gaetano Montelione, (Rutgers University, Piscataway) John Moult, (Institute for Bioscience and Biotechnology Research, Rockville) John Norvell, Maryland (Founding Director of the NIGMS Protein Structure Initiative) Dinakar Salunke, (Regional Centre for Biotechnology, Gurgaon) Gideon Schreiber, (Weizmann Institute, Rehovot, Israel) Joel L. Sussman, (Weizmann Institute, Rehovot, Israel) Janet Thornton, (European Bioinformatics Institute, Hinxton) Gunnar von Heijne, (Stockholm Bioinformatics Center, Stockholm) Ron Unger, (Bar-Ilan University, Ramat Gan) Shoshana Wodak (University of Toronto, Toronto) International Structural Genomics Organization Executive Committee Lucia Banci Aled Edwards Jennifer Martin Joel Sussman Tom Terwilliger Shigeyuki Yokoyama = = = = = =

1 0

Phenix.ensemble_refinment questions
by Joseph Brock 04 Dec '14

04 Dec '14

Dear Phenix community, I was hoping that some of you may be able to clarify some questions about Phenix.ensemble_refinement: 1. In the associated publication (Burnley et al. eLife 2012;), the ensemble refinement is validated by comparing the correlation of the ensemble generated map, with the map generated from the experimental phases for PDB entry 1YTT ("The overall correlation coefficient between the electron-density map from the ensemble model (obtained without experimental phases) and the experimentally phased electron-density map was 0.903, compared with 0.873 and 0.895 for the published and re-refined single structures. These seemingly small improvements in over- all quality indicators allow for significant local improvements."). I am confused how one computes an experimentally phased from structure factors deposited in the PDB that contain only anomalous intensities/amplitudes and not Hendrickson-Lattman coefficients. Is there a program within the phenix package that can do this? In addition, the phenix.ensemble_refinement keywords include: * experimental_phases * file_name = None * labels = None * Is it possible to include experimental phases during the rolling average refinement process and could this be beneficial (if the phases were of a sufficient quality)? 2. Is the correct procedure in parameter optimisation to optimise pTLS, then temperature offest and then tx? Or is it possible that the best ensemble may be generated from any (non-directional) combination of the above parameters? 3. What is the function of the "nproc" keyword? If this is the number of CPU cores that can be used in parallel, what is the most efficient way of using phenix.ensemble_refinement on a cluster? 4. Can anybody suggest a good way to compare the ensembles generated by phenix.ensemble_refinement with the trajectories of traditional MD simulations (for e.g. produced by NAMD? ;) Finally, I noticed that I cannot run phenix.ensemble_refinement using a "my_parameters.eff" file, it is necessary to type on the command line. Alternatively, the queueing system for the supercomputer I use is managed by SLURM, however, I cannot submit batch jobs via the appropriate command sbatch with anything other than default parameters (keywords in a parameters.eff or that are typed explicitly following the mycoords.pdb mydata.mtz myrestraints.cif files are not incorporated into the resulting parameters of the .log file). Could these issues be due to my local environment setup? I am running Phenix 1.9-1692 Platform: intel-linux-2.6-x86_64 redhat-e6.5. Sorry for the long email and many thanks in advance for you help! Best regards, Joseph. Joseph Brock | PhD Division of Physiological Chemistry II Department of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 SE-171 77 Stockholm, Sweden

6 9

Fwd: PostDoc position at the ALS
by Peter Zwart 03 Dec '14

03 Dec '14

Dear Colleagues, The Advanced Light Source in Berkeley is now looking to recruit two Postdocs to develop scattering in the tender X-ray regime. In particular using the Phosphors and Sulfur k-edge to enhance scattering. Details may be found here: *http://jobs.lbl.gov <http://jobs.lbl.gov/> * Postdoctoral Researcher - TReXS (Materials/ Physical Science)-80316 *and* Postdoctoral Researcher - TReXS (Biophysical Sciences)-80317 Alexander Hexemer and Peter Zwart Lawrence Berkeley National Lab -- ----------------------------------------------------------------- P.H. Zwart Staff Scientist Berkeley Center for Structural Biology, Science lead Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 SASTBX: http://sastbx.als.lbl.gov BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org -----------------------------------------------------------------

1 0

pdb file error
by maher alayyoubi 03 Dec '14

03 Dec '14

Hi Everyone, I am having a problem of phenix.refine not accepting a pdb file that I just finished editing in coot. It is a protein RNA compplex where the protein part was built in buccaneer and the RNA strand built in nautilus. I assembled the final model by text editing the pdb file and adding the RNA part. Whenever I feed this pdb file into phenix, it comes back with two errors: " number of atoms with unknown unbonded energy type symbols:6" . "The coot command could not be located" Does anyone know how to fix this problem? I tried converting the file into mmcif and feeding it to phenix but the same error comes back again. Thank you very much, Maher

2 1

norleucine (NLE) restraints
by Daniel Keedy 01 Dec '14

01 Dec '14

Hi everybody, First-time poster! I'm trying to re-refine 2f4k.pdb, but phenix.refine chokes on the non-standard norleucine (NLE) amino acid. I've tried phenix.elbow and phenix.ready_set using different version of PHENIX, with the NLE cards as either HETATM or ATOM, all to no avail. SHELX was used to refine the structure originally, but I'd like to use PHENIX to re-refine it. Any ideas on how to define these restraints? Daniel Keedy James Fraser Lab UCSF

3 3

来自"张士军" <[email protected]>的邮件
by 张士军 01 Dec '14

01 Dec '14

hello everyone how could use phenix phasing to phase a se substructure by search any possible spacegroup

1 0

Generate table 1-error message
by Lau Sze Yi (SIgN) 30 Nov '14

30 Nov '14

Hi, I got an error message when I tried to run the generate table 1 utility: Crystal symmetry mismatch between different files. My input files for pdb, mtz and cif were generated from my ccp4 refmac run. The unmerged data is the mtz output of ccp4 aimless. Did I upload the wrong file? Regards, Sze Yi Research Fellow Singapore Immunology Network (SigN) 8A Biomedical Grove, #03-06 Immunos, Singapore 138648 DID: +65 6407 0640 Fax: +65 6407 0640

2 1

Not a suitable array of R-free flags:
by Yamei Yu 27 Nov '14

27 Nov '14

Dear all, I use phenix.refine to refine a structure. Firstly, I used --dryrun to generate an .eff file. The command is "phenix.refine --dry_run 7_44.mtz 7_44.pdb refinement.input.xray_data.r_free_flags.generate=True refinement.input.xray_data.r_free_flags.max_free=1000” Then I use run the program by typing “phenix.refine 7_44_refine_001.eff” It runs correct! After that I use coot to modulate some parts of the structure, then I want to refine the structure again. I type “ phenix.refine 7_44_refine_002.def” This time I got the following error message: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=R-free-flags Sorry_Not_a_suitable_array: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=R-free-flags To override the suitability test define: refinement.input.xray_data.r_free_flags.disable_suitability_test=True I checked the generated file by phenix “7_44_refine_data.mtz” I does contain a column labeled as R-free-flags. I paste part if it below. * Space group = 'P1' (number 1) OVERALL FILE STATISTICS for resolution range 0.000 - 0.277 ======================= Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC -32 31 0 100.00 -2.2 11.9 49.44 1.90 H H 2 NONE -46 45 0 100.00 -2.5 17.8 49.44 1.90 H K 3 NONE 0 49 0 100.00 18.8 18.8 49.44 1.90 H L 4 NONE 0.9 271.3 0 100.00 26.52 26.52 49.44 1.90 F F-obs 5 NONE 0.2 5.1 0 100.00 1.25 1.25 49.44 1.90 Q SIGF-obs 6 NONE 0.0 1.0 0 100.00 0.01 0.01 49.44 1.90 I R-free-flags No. of reflections used in FILE STATISTICS 143215 Then I regenerate a new mtz file with FreeRflag by XDSCONT, then I revise the .def file accordingly and rerun the program. I got same error message:Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=FreeRflag Sorry_Not_a_suitable_array: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=FreeRflag To override the suitability test define: refinement.input.xray_data.r_free_flags.disable_suitability_test=True I checked my new mtz file, it dose contain a column labeled as FreeRflag Why there is an error message? How to solve it? Thank you so much!! Best wishes! yamei ************************************************ Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyuxtal(a)gmail.com ymyuxtal(a)163.com yamei_yu(a)scu.edu.cn

3 2

error messages running phenix.mr_rosetta
by Ursula Schulze-Gahmen 26 Nov '14

26 Nov '14

I am running mr_rosetta on a 64bit Linux computer. The model optimization worked without a problem, but now in the molecular replacement step I am receiving error messages, and I am not sure what the problem is. Could anyone provide a suggestion? Thanks Ursula /usr/share/themes/Slider/gtk-2.0/gtkrc:80: error: unexpected identifier `colorize_scrollbar', expected character `}' Fontconfig warning: no <cachedir> elements found. Check configuration. Fontconfig warning: adding <cachedir>/var/cache/fontconfig</cachedir> Fontconfig warning: adding <cachedir>~/.fontconfig</cachedir> (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): Pango-WARNING **: Failed to load Pango module '/programs/x86_64-linux/phenix/dev-1819/phenix-dev-1819/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so' for id 'BasicScriptEngineFc' (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): Gtk-WARNING **: Could not find the icon 'system-file-manager'. The 'hicolor' theme was not found either, perhaps you need to install it. You can get a copy from: http://icon-theme.freedesktop.org/releases -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

1 0

residue selection for rsrl?
by Kevin Jude 26 Nov '14

26 Nov '14

I am refining a structure at 2.9 Å resolution and have two side chains that keep moving out of density during reciprocal space refinement; both side chains should fit the resulting Fo-Fc density in favored rotamers. Turning on real-space refinement fixes this problem but leads to higher Rfree and poorer geometry overall. Can I select a subset of residues for real space refinement while still performing reciprocal space refinement on the whole asymmetric unit? Thanks for any help Kevin

2 2

phenix rosetta refine
by Andreas Förster 26 Nov '14

26 Nov '14

Dear all, I'm trying to get phenix.rosetta_refine to run. I think it's all set up properly, with Rosetta 3.5 and Phenix 1810 on RHEL 6.3 64bit. However phenix.rosetta_refine model.pdb data.mtz nproc=48 protocol=full > log& fails with the following error in log: End of input processing Sorry: The RosettaScripts executable could not be located. Please add the appropriate directory to your PATH environment variable, or set the variable ROSETTA_BIN to point to it. To me it seems things are defined correctly: andreas@csbstereo in phenix: echo $ROSETTA_BIN /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin andreas@csbstereo in phenix: ls $ROSETTA_BIN | grep scripts rosetta_scripts.linuxgccrelease@ rosetta_scripts.default.linuxgccrelease@ andreas@csbstereo in phenix: ll $ROSETTA_BIN/rosetta_scripts.linuxgccrelease lrwxrwxrwx 1 csbadmin csb 93 Oct 9 2013 /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -> ../build/src/release/linux/2.6/64/x86/gcc/4.4/default/rosetta_scripts.default.linuxgccrelease Any idea of what's wrong would be greatly appreciated. Andreas -- Andreas Förster X-ray Crystallography Facility Manager Centre for Structural Biology Imperial College London

3 2

Alternative conformation of ligand with near zero occupancy
by Singh, Bishal 26 Nov '14

26 Nov '14

Hello everybody, I thank you for clarifying my previous doubts. Your suggestions matter a lot to me. Here I have another doubt. I have structure of a protein in complex with triglycan (fucose-galactose-galactose). The terminal galactose of this triglycan possesses two conformations with occupancies 0.4 and 0.6. In order to satisfy the geometric parameters of this triglycan, I derived the alternative conformation of fucose and the central galactose as well. Then I performed occupancy refinement. The occupancy of alternative central galactose is 0.06 and that of alternative fucose is 0.00. Now the question is, should I delete this fucose of zero occupancy or keep it to maintain the geometric parameters of triglycan? I am looking forward for your opinion. If you like I can provide a snapshot of ligand with electron density. With regards, Bishal Singh PhD student DKFZ, University of Heidelberg, Germany

2 1

input for specifying labin in phenix.find_ncs
by Arka Chakraborty 26 Nov '14

26 Nov '14

Dear Phenix BBers, I have a seemingly trivial problem in specifying column labels in phenix.find_ncs. Following the manual, on entering labels as : phenix.find_ncs xx.pdb yy.mtz params.ncs.labin = "labin FP=F PHIB=PHI FOM=FOM" , phenix returns the error : 'Sorry, cannot interpret the keyword: params.ncs.labin=labin FP=F PHIB=PHI FOM=FOM'. Any clues on what mistake I might be making will be greatly appreciated. Thanks a lot, Regards, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*

3 4

Different space group of coordinate and structure factors
by Singh, Bishal 25 Nov '14

25 Nov '14

Hello everybody, For a data-set, the space group after data-processing was P4222. When I performed molecular replacement through PHASER in phenix keeping the search option 'All possible in same point group", the space group changed to P41212. Now the question is that shall I process the data again in this new space group or should I move on for refinement? Please suggest me your opinion. With regards, Bishal Singh PhD Student DKFZ, University of Heidelberg, Germany

2 2

explicit solvent in low resolution refinement
by Guenter Fritz 25 Nov '14

25 Nov '14

Dear all, we have determined the structure of a protein complex at 3.5 A resolution as well as the structures of three subunits of this complex independently at resolutions better than 2 A. I had used the models of the subunits as reference models in refinement, perfect. Now I was wondering whether one could use explicit solvent positions (e.g. inner shell water molecules) from the high resolution structures in the low resolution refinement. This should be superior to a simple bulk solvent model. I placed the inner shell water molecules from the high res structures into the low res model and added harmonic restraints to the water positions in low res refinement. I see a decrease of about 0.5% in Rwork and Rfree versus the model without water molecules. However, adding harmonic restraints excludes the option to use the reference models in refinement. Is it possible to use protein and water atoms from the reference models to generate restraints for the low resolution refinement? Thank you, Guenter

5 9

ready set and H/D addition on waters
by Maxime Cuypers 25 Nov '14

25 Nov '14

hello, after not using phenix for a while, i just realised the new versions do not include the option in ready_set gui to add H or D atoms to waters in the pdb models (and only to the waters without altering the rest of the model would be nice). of course it can be done on the command line but why has it been removed? it is a very neutron crystallographer friendly option don t you think? cheerios, -- Dr. Maxime Cuypers

3 4

Rwork > Rfree
by Singh, Bishal 21 Nov '14

21 Nov '14

Hello everybody, While depositing a structure in PDB, I observed that Rwork was more than Rfree in the highest resolution shell and in a few more shells as well. I shall be delighted if somebody can suggest me the reasons and also what should I do now. With regards, Bishal PhD student, DKFZ, University of Heidelberg, Germany

4 3

MRage against local "select" PDB database on commandline
by Kaushik Hatti 21 Nov '14

21 Nov '14

Hi, I am new to Phenix. Sorry if my question is naive. For a given mtz file, I want to pick templates from a local PDB database (its actually iTasser template library) and perform Molecular Replacement using MRage. I have already installed Blast, downloaded iTasser PDB library (http://zhanglab.ccmb.med.umich.edu/library/PDB.tar.bz2) and extracted sequences from both the downloaded PDB template library set and target protein for which mtz is available. How should I go about building pipeline to perform MR using templates from locally downloaded select PDB database? Are there any more parameters available for parameter name: services under scop: search other than "local" and "ncbi"? Thanks in advance, Kaushik -- People living deeply have no fear of death - Anais Nin Caution: I am still the dumbest person I have ever known :-)

2 6

Submissions for Comput. Cryst. Newsletter
by Nigel Moriarty 20 Nov '14

20 Nov '14

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission in the January 2015 issue is 17 December 2014 (with some leeway if you are still working on the text, especially as it can be polished over the break). The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

1 0

Re: [phenixbb] Rwork > Rfree
by Ed Pozharski 20 Nov '14

20 Nov '14

Generate a different test set and repeat refinement. Do it twenty times. If R turns out to be systematically higher than Rfree even in few resolution shells, you have an interesting case worth looking at. If not, it's just noise. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: "Singh, Bishal" <b.singh(a)dkfz-heidelberg.de> </div><div>Date:11/20/2014 9:52 AM (GMT-05:00) </div><div>To: phenixbb(a)phenix-online.org </div><div>Subject: [phenixbb] Rwork > Rfree </div><div> </div>Hello everybody, While depositing a structure in PDB, I observed that Rwork was more than Rfree in the highest resolution shell and in a few more shells as well. I shall be delighted if somebody can suggest me the reasons and also what should I do now. With regards, Bishal PhD student, DKFZ, University of Heidelberg, Germany _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

1 0

GeoStd: was definition of glycosylation in phenix.refine
by Schubert, Carsten [JRDUS] 18 Nov '14

18 Nov '14

Hi Nigel, could you please comment on any plans to harmonize the use of these restraints for other refinement programs as well. Phenix originally appears to have implemented the restraint dictionaries from CCP4. Right now there seems to be some kind of parallel development going on with the dictionaries being in sync to some degree. Is there a plan to move to a unified restraints distribution at some point? Thanks Carsten From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Nigel Moriarty Sent: Tuesday, November 18, 2014 12:38 PM Cc: PHENIX user mailing list Subject: Re: [phenixbb] definition of glycosylation in phenix.refine @Laurent Engin advice is sound but you are having trouble free feel to send me the inputs directly. NB. Any files sent to me will be held in strictest confidence. @Engin I think you will find what you are looking for in the GeoStd. As restraints are improved, they are moved from $PHENIX/chem_data/mon_lib to $PHENIX/chem_data/geostd (which is hosted on SourceForge for anybody's use). The directory structure is the same as the Monomer Library with a geostd_list.cif file corresponding to mon_lib_list.cif which specifies the links. Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov<mailto:[email protected]> Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> On Tue, Nov 18, 2014 at 8:25 AM, Engin Özkan <eozkan(a)uchicago.edu<mailto:[email protected]>> wrote: Hi Laurent, If I am reading the error message right, you did not delete the hydrogens that get removed upon bond formation. That's what it is complaining about. I always thought Phenix probably removed these atoms (the hydroxyl and the hydrogen) automatically when you defined the link, but never tested if it really does it. I also usually remove all hydrogens right away when sugar residues are inserted. Finally, I will recommend that you use automatic linking in the phenix.refine GUI. It works great (I am on the latest nightly, dev-1839; you may need to upgrade). No need to define pesky links anymore. Thank you developers! At the risk of hijacking the thread, I could not find in my installation the cif files for N-linked sugars. Have they been moved elsewhere? Hope this helps, Engin On 11/18/14 10:02 AM, Laurent Maveyraud wrote: Hi, I am currently refining a structure of a glycosylated protein, but I fail to define the appropriate links... The glycosylatin is Asn638-NAG1061-(beta1-4)-NAG1062-(beta1-4)-BMA1063-(ALPHA1-3)-MAN1064 This is what I add in the eff file : apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain D and resname NAG and resid 1061 residue_selection_2 = chain A and resname ASN and resid 638 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain D and resname NAG and resid 1062 residue_selection_2 = chain D and resname NAG and resid 1061 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain D and resname BMA and resid 1063 residue_selection_2 = chain D and resname NAG and resid 1062 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain D and resname MAN and resid 1064 residue_selection_2 = chain D and resname BMA and resid 1063 } this is correctly read in refine: apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain D and resname NAG and resid 1061 residue_selection_2: chain A and resname ASN and resid 638 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain D and resname NAG and resid 1062 residue_selection_2: chain D and resname NAG and resid 1061 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain D and resname BMA and resid 1063 residue_selection_2: chain D and resname NAG and resid 1062 apply_cif_link: data_link: ALPHA1-3 mod_id_1: DEL-HO3 mod_id_2: DEL-O1 residue_selection_1: chain D and resname MAN and resid 1064 residue_selection_2: chain D and resname BMA and resid 1063 but generates an error : Number of atoms with unknown nonbonded energy type symbols: 5 "HETATM10951 HO4 NAG D1052 .*. H " "HETATM10973 HO4 BMA D1053 .*. H " "HETATM11028 HO4 NAG D1062 .*. H " "HETATM11050 HO4 BMA D1063 .*. H " "HETATM11070 HO3 MAN D1064 .*. H " and the job stops. Any ideas on what if wrong ? thanks for your help Laurent _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb

1 0

definition of glycosylation in phenix.refine
by Laurent Maveyraud 18 Nov '14

18 Nov '14

Hi, I am currently refining a structure of a glycosylated protein, but I fail to define the appropriate links... The glycosylatin is Asn638-NAG1061-(beta1-4)-NAG1062-(beta1-4)-BMA1063-(ALPHA1-3)-MAN1064 This is what I add in the eff file : apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain D and resname NAG and resid 1061 residue_selection_2 = chain A and resname ASN and resid 638 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain D and resname NAG and resid 1062 residue_selection_2 = chain D and resname NAG and resid 1061 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain D and resname BMA and resid 1063 residue_selection_2 = chain D and resname NAG and resid 1062 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain D and resname MAN and resid 1064 residue_selection_2 = chain D and resname BMA and resid 1063 } this is correctly read in refine: apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain D and resname NAG and resid 1061 residue_selection_2: chain A and resname ASN and resid 638 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain D and resname NAG and resid 1062 residue_selection_2: chain D and resname NAG and resid 1061 apply_cif_link: data_link: BETA1-4 mod_id_1: DEL-HO4 mod_id_2: DEL-O1 residue_selection_1: chain D and resname BMA and resid 1063 residue_selection_2: chain D and resname NAG and resid 1062 apply_cif_link: data_link: ALPHA1-3 mod_id_1: DEL-HO3 mod_id_2: DEL-O1 residue_selection_1: chain D and resname MAN and resid 1064 residue_selection_2: chain D and resname BMA and resid 1063 but generates an error : Number of atoms with unknown nonbonded energy type symbols: 5 "HETATM10951 HO4 NAG D1052 .*. H " "HETATM10973 HO4 BMA D1053 .*. H " "HETATM11028 HO4 NAG D1062 .*. H " "HETATM11050 HO4 BMA D1063 .*. H " "HETATM11070 HO3 MAN D1064 .*. H " and the job stops. Any ideas on what if wrong ? thanks for your help Laurent -- ---------------------------------------------------------- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr P I C T --- Plateforme Intégrée de Criblage de Toulouse Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département Biologie Structurale et Biophysique http://cribligand.ipbs.fr http://www.ipbs.fr 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 ----------------------------------------------------------

3 3

mrage with nucleic acids?
by Paul Paukstelis 17 Nov '14

17 Nov '14

I'm trying to run mrage with nucleic acid models. With phaser, it is possible to specify the molecule type, but this option doesn't exist in mrage (from what I can see). Providing a sequence file automatically assumes protein one letter codes. Any suggestion on how to clearly define a sequence file as a nucleic acid? Thanks, --paul

2 1

Filtering CCP4 maps to lower resolution
by Barad, Ben 16 Nov '14

16 Nov '14

Hi All, I am currently trying to filter a CCP4-formatted real space map from the EMDB, which is at 3.2 Å resolution, to different resolutions from 3.2 to 5 Å, and I've been having a bit of a difficult time getting it to work. My first thought was to do an fft to get structure factors, then regenerate the map from those structure factors with a resolution cutoff. To do this, I used the tools "phenix.map_to_structure_factors" and "phenix.mtz2map" to generate a structure factor file, then convert it back into a map. When I do this, I end up with a very noisy map that is not usable for what I would like to do. Is there a better way to accomplish this in phenix (or another tool)? I've also tried some low-pass filtering with proc3d, without much success... Thanks, Ben Barad Fraser Lab @ UCSF

3 3

Re: [phenixbb] simulated annealing omit map
by Pavel Afonine 15 Nov '14

15 Nov '14

Hello Bishal, as discussed before, computing ligand-omit map is tricky. Quoting my previous email: """ There are two commonly used options for omitting the ligand in order to demonstrate its presence/absence in Fo-Fc OMIT map: 1) Physically remove the ligand from PDB file. Then do some refinement and calculate Fo-Fc map. 2) Keep ligand in the file, set its occupancy to zero. Then, again, do some refinement and calculate Fo-Fc map. In this case you may want to ask refinement program to not move the ligand or move it only a little. Now, here is why these two options are poor and will not give you what you want. In the first case the bulk-solvent mask will be set in the ligand region and therefore it will mask ligand density (bulk-solvent will be filled into the ligand region). Depending on the strength of ligand density it may be masked completely or deteriorated. If you follow the second option you will always get positive density in ligand area. This density may correspond to bulk-solvent, ligand or mixture of both. That is there will be no simple way to differentiate whether this density arises from the ligand or bulk-solvent. """ Dale Tronrud offered a great alternative option: """ An alternative you might want to consider is what I call the "discovery map". At some point in the refinement process there was a map that convinced YOU that this ligand was present. You should be the hardest person to be convinced so that map will be both an omit map (because the model had been refined without the ligand prior to this) and clear enough to satisfy the reader. """ Now, recently I improved composite OMIT map calculation in phenix.composite_omit_map tool, see picture that illustrates how it works: https://www.dropbox.com/s/dbp8e0348v5p78h/fig_6.png?dl=0 I think at present that's the best option to follow if for some reason you cannot follow Dale's suggestion. Pavel On 11/13/14 6:58 AM, Singh, Bishal wrote: > Hello everybody, > I am generating figures showing the electron density map around the > ligands. I deleted the ligands from final co-ordinate file and then > performed refinement with identical parameters as before while > keeping simulated annealing=true. I shall be thankful if someone could > suggest me whether I consider mFo-DFc map or 2mFo-DFc map or both. > Kindly also tell me the minimum acceptable contour level required for > showing difference map. All structures are at 1.4 - 2.0 angstrom > resolutions. > > Regards, > Bishal

5 5

CB outliers
by George Devaniranjan 14 Nov '14

14 Nov '14

Hi, I refined a structure using phenix.refine. The R/R free decreased slightly from 13.46/15.87 to 13.0/15.6. But, molprobity said there were 3 CB outliers (starting from 0). I looked at those residues in COOT. I could NOT really see a different between the refined and initial model. In addition I looked at COOT validate-->density fit analysis I cannot see ANY difference in the peak heights (same numerical value too). I looked at RSCC (using phenix validate tools as well). I still can't see a difference in the plots. I am not sure how to get rid of the 3 CB outliers that have crept in since I can't pick them out as worse off in the refined model. I ask since in another case > 3 CB outliers, with the same results in picking them out in COOT/RSCC. I am wondering if there is another way I can see the deviation and fix it? Thank you, George

3 6

Rosetta compile problem
by miyatake 13 Nov '14

13 Nov '14

Dear all, I tried to compile Rosetta for rosetta_refinement, on Mac OX10.10. I run " /rosetta_2014.22.56873_bundle/main/source] user% sudo scons.py But it was in failure, showing the following message: g++-4.2 -o build/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/cppdb/atomic_counter.os -c -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 -m64 -march=nocona -mtune=generic -O0 -g -ggdb -ffloat-store -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_SUFFIX=\".dylib\" -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_DISABLE_SHARED_OBJECT_LOADING -DCPPDB_DISABLE_THREAD_SAFETY -DCPPDB_SOVERSION=\"0\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -Ibuild/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/sqlite3 -Iexternal/dbio/sqlite3 -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include external/dbio/cppdb/atomic_counter.cpp sh: g++-4.2: command not found scons: *** [build/external/debug/macos/14.0/64/x86/gcc/4.2/default/dbio/cppdb/atomic_counter.os] Error 127 scons: building terminated because of errors. How can I resolve that? Best regards, H. Miyatake

3 2

simulated annealing omit map
by Singh, Bishal 13 Nov '14

13 Nov '14

Hello everybody, I am generating figures showing the electron density map around the ligands. I deleted the ligands from final co-ordinate file and then performed refinement with identical parameters as before while keeping simulated annealing=true. I shall be thankful if someone could suggest me whether I consider mFo-DFc map or 2mFo-DFc map or both. Kindly also tell me the minimum acceptable contour level required for showing difference map. All structures are at 1.4 - 2.0 angstrom resolutions. Regards, Bishal

1 0

Settings-Directories of MR-Rosetta wizard is altered when phenix-GUI is restarted?
by Martin Moche 13 Nov '14

13 Nov '14

Dear colleagues, When restarting phenix followed by opening the "MR-Rosetta(beta)" the Settings-Directories need to be reset each time? How can I set Rosetta binary directory name: Rosetta binary name: Rosetta script directory name: Rosetta database directory name: in Settings-Directories of "MR-Rosetta(beta)" wizard (or elsewhere) so that they do not change each time I restart the phenix-GUI? These settings are not changed: Base output folder: Rosetta path: Likely "Rosetta path" does not change between phenix-GUI restarts since PHENIX_ROSETTA_PATH is set in the shell as: echo $PHENIX_ROSETTA_PATH /software/apps/rosetta/2014.35/gcc01/rosetta_2014.35.57232_bundle The "Path to Rosetta" in "Phenix preferences - Wizards" is currently left blank since $PHENIX_ROSETTA_PATH is set in the shell. I have by accident started a few jobs with mixed (new and old) settings and phenix-GUI starts without error messages and all processors are running 100% CPU, however likely in some infinite loop since no work is performed beyond "place model"... Best regards, Martin Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: Martin.Moche(a)ki.se

1 0

fix atoms during refinement
by CPMAS Chen 10 Nov '14

10 Nov '14

Dear All Phenix Users, Is there a way to fix certain atoms position during refinement? I have some heavy atoms identified with MR-SAD, but when I build the whole molecule and have phenix to refine its position, the heavy atom's position is shifted from the anomalous signal. Therefore I would like to have these heavy atoms positions fixed during refinement. Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

2 1

Ringer
by Ivan IVANOV 10 Nov '14

10 Nov '14

Dear All, I am trying to use ringer with a model I have. I followed the tutorial for Calmodulin and it worked very well for my protein. (http://bl831.als.lbl.gov/ringer/ringer/Tutorial/tutorial.htm). Now I have all files sigma vs chi angles for the residues I want and also the list of peaks identified above the sigma cutoff I selected. I am struggling to analyse the outputs as it is shown on the calmodulin exemple. I found this website (http://bl831.als.lbl.gov/ringer/ringer/Documentation/ringerManual.htm#Userp…) which is explaining very briefly how to plot all different conformation vs chi angles and how to show all selected amino acid conformation in the electron density (4.4 Plotting Accessory). I have to admit that this is not straigthforward for me to plot all outputs in a comprehensive way. Does anyone of you have a script to run with ringer outputs and get the final figures as it is shown on both websites ?? Kind regards, Ivan -- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 71, avenue des Martyrs CS 90181 38042 Grenoble Cedex 9 T: +33 (0)4 76 20 7630 T(lab): +33 (0)4 76 20 7014 Email: ivanov(a)embl.fr Url: http://www.embl.fr

3 2

"Femtosecond crystallography of membrane proteins in lipidic cubic phase (LCP)” Webinar
by Angela Criswell 04 Nov '14

04 Nov '14

Dear colleagues, I would like to draw your attention to an upcoming free, educational webinar to be presented by Dr. Wei Liu titled “Femtosecond crystallography of membrane proteins in lipidic cubic phase (LCP).” Despite recent technological advances in heterologous expression, stabilization and crystallization of membrane proteins, structural studies remain difficult. Wei’s presentation will describe the use of serial femtosecond crystallography of membrane proteins in LCP and how this approach holds promise to interrogate this difficult, yet important, class of proteins. This webinar is scheduled to occur on Thursday, November 13th at 11:00 AM CST (9:00 AM PST / 5:00 PM GMT). You can find an abstract and registration link for this webinar at: http://www.rigaku.com/webinars. We hope you will join us for the event. Best regards, Angela Criswell -- Angela Criswell VP, Life Science X-ray Products Rigaku Americas Corporation 9009 New Trails Drive The Woodlands, TX 77381 USA Ph: +1 281 362 2300 ext. 216 Fax: +1 281 364 3628 Email: angela.criswell(a)rigaku.com URL: http://www.rigaku.com Subscribe to Rigaku eNewsletters<http://www.rigaku.com/subscribe>

1 0

green ball in aspartate
by Murpholino Peligro 31 Oct '14

31 Oct '14

Hi Everybody. Does anybody knows what could this be? Blue map at 1rmsd Green and red map at 3.5 rmsd Purple map (FEM map) at 1rmsd Conditions 100mM sodium acetate, NaCl 10% w/v, cryo=glycerol 30 % v/v; protein is hen egg white lysozyme (usual condition, usual protein and ohh..almost forget it.. ascorbic acid at 0.5 M) A water molecule overlaps with the oxygen atom (OD1) of the aspartate residue. So it is not a water molecule. Any ideas? (In coot -> validate-> difference map peaks and holes-> its the only one at 7.7 rmsd) Thanks

2 1

[ot]: nedit on Mac 10.10 yosemite
by Sebastiano Pasqualato 29 Oct '14

29 Oct '14

Hi folks, sorry for the off-topic and slightly ‘demodée’ question, but, since I updated to Yosemite on my Mac, "nedit" does not work any more. Here’s the error message: Seba@host041:~> nedit dyld: Library not loaded: /usr/X11R6/lib/libXp.6.dylib Referenced from: /Applications/nedit/nedit Reason: image not found Trace/BPT trap: 5 Seba@host041:~> Anybody knows if there is a fix for that? Thanks in advance, S -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_XtalUnit

3 3

Fwd: Postdoc position in acoustic crystal preparation and high throughput screening at NSLS II
by Nathaniel Echols 28 Oct '14

28 Oct '14

---------- Forwarded message ---------- From: "Soares, Alexei" <soares(a)bnl.gov> To: "CCP4BB(a)JISCMAIL.AC.UK" <CCP4BB(a)jiscmail.ac.uk>, "cnsbb(a)yahoogroups.com" <cnsbb(a)yahoogroups.com>, "pdb-l(a)rcsb.org" <pdb-l(a)rcsb.org>, " phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org>, " x-plor(a)net.bio.net" <x-plor(a)magpie.bio.indiana.edu>, "xtal-log(a)net.bio.net" <xtal-log(a)magpie.bio.indiana.edu> Cc: Date: Tue, 28 Oct 2014 14:44:30 +0000 Subject: Postdoc position in acoustic crystal preparation and high throughput screening at NSLS II *Postdoctoral Research Associate – Macromolecular Crystal Preparation for NSLS-II* *2-year Term Position* *BNL Overview:* Brookhaven National Laboratory is a nonprofit research and development institution whose purpose is to advance ideas and knowledge through a multidisciplinary program of basic and applied research. *Project Overview:* A postdoctoral position is available to develop new crystal-preparation technologies to advance the use of serial macromolecular crystallography (MX) at NSLS-II. This new synchrotron will soon begin operation at Brookhaven National Laboratory. The individual will develop technologies for crystallization, drug discovery, and crystal handling to make serial crystallography possible, using various technologies, including acoustic droplet ejection (ADE). The project will provide the capability for experimenters to employ nanoliter quantities of material to produce specimens for diffraction studies with a large number of discrete experiments in a small area. This will exploit the micro-beam capabilities of NSLS-II MX beamlines; both room temperature and cryogenic serial crystallography strategies will be explored. High-throughput screening will be used for different types of structural biology projects (crystallization conditions, fragment binding, etc). The individual will work closely with a broad technology-development team. Our team members have different areas of expertise, from 3D labware design to research on medically relevant expressed proteins. No experience with ADE is necessary. *Essential Duties and Responsibilities:* The successful candidate will assist in the development and implementation of procedures and computer algorithms that leverage the Echo 550 instrument for macromolecular crystallography applications for serial crystallography applications in the few-nanoliter regime. The candidate will also develop novel technologies as well as improve existing technologies, and will have opportunities to participate in other related projects in a large and diverse group. *Required Knowledge, Skills and Abilities:* - Ph.D. in an appropriate chemistry, biology, or physics discipline; structural biology, crystallography, or a related field will have preference - Demonstrated experience (preferably including publications) in innovative experimentation and/or methods development with crystallography or drug discovery - Experience with conventional crystallization, and familiarity with micro crystallization and handling of micro crystals will be valuable - Experience in computer programming - The candidate must have a demonstrated ability to work with a team. *Other Information:* BNL policy states that Research Associate appointments may be made to those who have received their doctoral degrees within the past five years. *Please apply to Job # 137 on our jobs website:* *http://www.bnl.gov/HR/careers/ <http://www.bnl.gov/HR/careers/> * At Brookhaven National Laboratory we believe that a comprehensive employee benefits program is an important and meaningful part of the compensation employees receive. Our benefits program includes but is not limited to: - Medical Plans - Vacation - Holidays - Dental Plans - Life Insurance - 401(k) Plan - On-site Child Development Center, Swimming Pool, Weight room Tennis Courts, and many other employee perks and benefits.

1 0

R/R free reported values
by Cedric 28 Oct '14

28 Oct '14

Hi Phenix and CCP4 community, (sorry for the cross posting). I was looking at a PDB file. The http://www.rcsb.org/ website page gives the following values: R-Value: 0.103 (work) R-Free: 0.134 The actual PDB file gives the following: R :0.110 FREE R VALUE : 0.170 I was wondering why the difference. The structure is 1.0A resolution 2CWS. Thank you, ____________________________________________________________ FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more!

6 7

difference between phenix.mrage and phenix.MRage?
by Murpholino Peligro 27 Oct '14

27 Oct '14

? Thanks

2 1

Cacodylate won't stay in place
by Kgosisejo, Oarabile 27 Oct '14

27 Oct '14

Hello all, I am trying to fit cacodylate ion in my model using Coot but it does not stay where I put it. The molecule breaks apart and some of its components attach to the peptide residues. Due to this, phenix.refine would not accept this as the input for refinement. Is there a way I can make cacodylate ion stay in its electron density and refine my structure with cacodylate ion? I appreciate your help! Best Regards, Oarabile M. Kgosisejo o.kgosisejo(a)usask.ca

2 1

help on MIR dataset
by Ni, Fengyun 25 Oct '14

25 Oct '14

Hi everyone, I am working on a MIR dataset: one native data, three EMTS soaked data at different concentration, one PbAc2 data. My initial trial with phenix autosol did not give positive solutions. I hope I could get some information from all of you. I index and integrate the data in Mosflm and possible group is P3, though the Pointless said the most possible is P3121. But for now, I only tried P3 at different resolutions for the reason that a potential MR solution (below 20% identities, TFZ=7.1) was found in P31 space group. If P3121 is the real space group, the space is too crowed to fit my molecules unless they have some unexpected symmetry. For the difference among dataset in P3 space group, the output from SCALEIT of CCP4 gives as follows, RMS differences|RMSiso RMSano ---------------------------------------- FP-hg |172.30 22.50 FP-hg2 |159.20 24.07 FP-hg3 |85.08 27.92 FP-pb |31.15 24.55 The native data's resolution cutoff is 3.2 A, and 3.2/3.8/3.5 for different EMTS data, 3.5 for Pb data.I did notice some radiation damage for EMTS (Hg) data (large negative B-factors in SCALA), but not for Pb data. And the anomalous signal only extend to 5.6 and 4.5 A for EMTS and Pb data, respectively, as indicated by phenix.xtriage. These are all the possible heavy atom data we could obtain. So i tried all of them in phenix.autosol. The input is like follows, autosol { seq_file = ../seq.dat crystal_info { solvent_fraction = 0.62 #determined from matthews coefficient to assure "reasonable" content in asymmetric unit. } native { data = nat.mtz } deriv { data = hg1.mtz atom_type = Hg inano = noinano *inano anoonly lambda = 1.00394 } deriv { data = hg2.mtz atom_type = Hg inano = noinano *inano anoonly lambda = 1.00394 } deriv { data = hg3.mtz atom_type = Hg inano = noinano *inano anoonly lambda = 1.00394 } deriv { data = pb.mtz atom_type = Pb inano = noinano *inano anoonly lambda = 0.94640 } model_building { build = False #my structure is DNA/protein complex, so i choose to stop the building process. } } I tried at different resolutions, 3.6/4.0/4.4/4.8/5.2/5.6/6.0 A. One solution was given based on Pb data at 4.8 A with following statistics, Solution # 6 BAYES-CC: 59.7 +/- 17.2 (2SD) Dataset #4 FOM: 0.24 Score type: SKEW CORR_RMS NCS_OVERLAP Raw scores: 0.31 0.69 0.00 100x EST OF CC: 59.74 17.55 31.25 Refined heavy atom sites (fractional): X Y Z xyz 0.033 0.020 0.538 xyz 0.417 0.217 0.113 xyz 0.041 0.010 0.721 The statistics is almost the same for its inverse, and i read from the output that the statistics for phasing other Hg datasets are very low (BAYES-CC is lower than 20) based on the above solution. The resulting map does not make much sense yet. Sorry for the long post. Any suggestion is welcome. Thank you very much! Fengyun

2 8

pdb deposition
by Sneha Rangarajan 24 Oct '14

24 Oct '14

Hi everyone, For a 1.9A dataset, here are my statistics- Rfactors: 22/26 Ramachandran favored: 90.60% Ramachandran outliers: 2.17% Rotamer outliers: 4% Clashscore: 8 Bonds: 0.007 Angles: 1.2 I have tried a couple of things to refine it further but nothing seems to improve all the parameters. My question is what is an acceptable Rfactor at this resolution for deposition in pdb? Thanks, Sneha

2 1

how to refine everything except n residues in phenix.refine?
by Murpholino Peligro 23 Oct '14

23 Oct '14

Hi everybody! Everytime when I (within coot) do "real space refine" two arginines that have two alternate conformations ..(interacting by hydrogen bonds); and then phenix.refine everything, both conformers move away. Therefore, when I open my mtz and pdb files from phenix.refine in coot, I'll have green blobs where there should be guanidium groups. Can I tell phenix.refine not to move only those two residues? It should be something like the following lines in the eff file? sites { individual = None torsion_angles = None rigid_body = None remove_selection=resid 45 remove_selection=resid 68 } Thank you very much

4 8

Electrostatic potential map/Delphi/PDB2PQR
by Ivan IVANOV 21 Oct '14

21 Oct '14

Dear All, I am facing a problem. I have a protein-RNA complex at 2A resolution I refined using TLS in Phenix. Now in the pdb file I have ANISOU line for every atom and probably many other errors. This is the reason I am not able to run Delphi or PDB2PQR to create potential electrostatic map. I removed already all water molecules and all heteratoms and ANISOU lines and RNA molecule. The program creating the phi file for the potentials does not work at all. Do you know any server which can correct any errors in the pdb file in order to run properly the program to create electrostatic map ?? Thanks a lot, Ivan -- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 71, avenue des Martyrs CS 90181 38042 Grenoble Cedex 9 T: +33 (0)4 76 20 7630 T(lab): +33 (0)4 76 20 7014 Email: ivanov(a)embl.fr Url: http://www.embl.fr

3 2

An old (?) tutorial?
by Bryan Lepore 21 Oct '14

21 Oct '14

Greetings - On the public webpage, there used to be an outstanding text tutorial under the phenix.refine link (I think!) that described the attachment of prosthetic groups and such to protein, I think using NAG (or was it something else...). It had all the commands for inclusion in the .def. and of course I can't find it now on the public site. Should I look in the local docs of an old release? -Bryan

2 2

Phenix Table 1 discrepancy
by Rich Grey 20 Oct '14

20 Oct '14

I'm preparing Table 1 for a structure I have recently solved. I chose to compare the Table 1 Phenix produces to the data found in the PDB file and the log file from my last refinement in Phenix. I see discrepancies between the data for the highest resolution bin's R-factors, including what resolution data that bin contains. In addition, the number of reflections used in refinement is different (although only by about 5, so not a large difference). The PDB file appears to match the log file, and the overall Rwork and Rfree agree for all. Does anyone know where the Table 1 program in Phenix pulls these values from why I may be seeing these differences? Thank You. -Rich

2 1

anomalous signal
by Matteo Colombo 20 Oct '14

20 Oct '14

Hello, I was wondering if the f'' determined by XANES experiment is quantitatively significant and if it can be contributed by two different anomalous scatterers. For example in my protein I know that Co and Zn are present. In theory, at Zn absorption edge, I have a contribution from Co too. If I perform a XANES experiment to determine Zn absorption edge and I obtain a f'' of 5.87, does this value correspond to only Zn signal or to a sum of Zn+Co? Thanks a lot Matteo -- Matteo Colombo PhD Groupe Extremophile et grands assemblages moléculaire Institut de Biologie Structurale 71 avenue des Martyrs CS 10090 38044 Grenoble Cedex 9

4 4

phenix error
by Ivan IVANOV 17 Oct '14

17 Oct '14

Dear all, I have an error appearing in phenix. I think it is a problem of my pdb file. I do not know how to change it. Error: residue.id_str(suppress_segid=false):segid is not unique: pdbres=ATP C 1 "segid= "O" Does anyone can help me?? Where is the mistake and how to solve it ?? Kind regards, Ivan -- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 71, avenue des Martyrs CS 90181 38042 Grenoble Cedex 9 T: +33 (0)4 76 20 7630 T(lab): +33 (0)4 76 20 7014 Email: ivanov(a)embl.fr Url: http://www.embl.fr

3 2

Re: [phenixbb] COOT and default dictionary
by Yazan Abbas 16 Oct '14

16 Oct '14

Hi, I was trying to troubleshoot this and it seems to be a problem related to the FEM map only. When I open my FEM.mtz and do RSR in coot it works well if I choose the 2mFoDfc map but not the FEM map. I'm still not sure why it stopped working since coot was behaving normally just yesterday. Maybe it had something to do with the cif file I tried to import earlier (see previous message). Yazan PS I'm replying to my previously sent message, I hope it ends up in the same thread... On Thu, Oct 16, 2014 at 11:41 AM, Yazan Abbas <yazan.abbas(a)mail.mcgill.ca> wrote: > Hi, > > I am encountering a problem with coot real space refinement (RSR). > Basically when I try to fit any residues using RSR the atoms come apart and > fit into the center of the density, possibly because it is not reading in > any geometry restraints. This happens for examples when I am opening my > FEM .mtz map (either manually or 'open in coot' via phenix). > > The only times coot RSR behaves normally is when I load it via phenix > after running phenix refine, or when I open coot via the command line and > auto-open an mtz (the same one generated by phenix refine). Also, fetching > a pdb and map via EDA/PDBredo still allows me to use RSR. > > When I encountered the problem I tried to reinstall coot 0.8 stable and > also tried to install the latest pre (0.8.1-5404), and upgraded to phenix > 1.9-1692. My coot installation comes from the stand alone packages of the > Scott lab website. > > The only thing I can think of as having caused this is when I was trying > to fit an unusual ligand into my density, I used phenix elbow to generate a > cif file and then loaded that into coot (--> import cif dictionary). > Shortly afterwards coot gave up on real space refinement under most > circumstances. > > Have I somehow replaced a default dictionary file? > > Thanks, > > Yazan > > > -- > PhD Candidate > Dr. Bhushan Nagar Lab > McGill University > Tel: (514)-398-7271 > http://bhushan-nagar.lab.mcgill.ca/ > -- PhD Candidate Dr. Bhushan Nagar Lab McGill University Tel: (514)-398-7271 http://bhushan-nagar.lab.mcgill.ca/

2 1

R-factor difference between phenix and sftools
by Simon Jenni 13 Oct '14

13 Oct '14

Hi, we refined a structure in phenix.refine (dev-1810) and the R-factors are: Final R-work = 0.3221, R-free = 0.3638 phenix.cc_star agrees: phenix.cc_star com_001.pdb com_001.mtz \ f_obs_labels="F-obs,SIGF-obs" \ f_model_labels="F-model,PHIF-model" \ unmerged_data="xscale.hkl" r_work: 0.322 r_free: 0.364 so does phenix.model_vs_data: phenix.model_vs_data com_001.pdb com_001.mtz r_work : 0.3221 r_free : 0.3638 sigma_cutoff : None However, when I calculate the R-factors with sftools, I get a discrepancy between the phenix and sftools results: sftools << eof read com_001_f_model.mtz Y select col R_FREE_FLAGS > 0 correl col FOBS FMODEL select invert correl col FOBS FMODEL quit Y eof R-work: 33.6 R-free: 38.1 Does anyone perhaps know what causes this difference? With best regards, Simon PS: The structure is in spacegroup P212121 with strong pseudocentering tNCS (dimer in the asymmetric unit, native Patterson peak at 0.500 0.500 0.497). No indication for a P21 twin (L-test and refinement in P21 with twin law), not higher symmetry spacegroup I222 (alternating strong and weak reflections are visible in the diffraction patterns, resolved structural differences in the two protomers of the dimer). Two datasets from different beamlines. As might be expected, the R-factors after refinement are unusually high (e.g. 28/35 [conventional resolution cutoff at 3.1 A], 32/36 with Kay's CC cufoff at 2.6 A). I wanted to compare refinements between different programs to see how they cope with the unexpected bimodal amplitude distribution.

4 8

ligand fitting
by Sneha Rangarajan 13 Oct '14

13 Oct '14

Hello everyone, I have a question about ligand fitting into density. At this point my maps look quite good with decent density for the peptide (ligand)[Rfactprs 26/31]. I tried using ligandfit by giving it the pdb and mtz of the ligand free model along with peptide.pdb (peptide stripped from a pdb where it was complexed with a homologous protein). However the output was a ligand.pdb file with a CC of 0.49. I am not sure how to interpret this. Does this mean it could not find the density for the ligand? Is there a better way to fit the peptide into density? Thanks, S From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of Sneha Rangarajan Sent: Wednesday, October 08, 2014 10:30 AM To: Nathaniel Echols Cc: phenixbb(a)phenix-online.org Subject: Re: [phenixbb] (no subject) This was a great idea. My Rfactors after a second round of autobuild are now 25/32. I think it might be getting there afterall ☺ S From: Nathaniel Echols [mailto:[email protected]] Sent: Friday, October 03, 2014 3:08 PM To: Sneha Rangarajan Cc: Pavel Afonine; phenixbb(a)phenix-online.org<mailto:[email protected]> Subject: Re: [phenixbb] (no subject) On Fri, Oct 3, 2014 at 11:58 AM, Sneha Rangarajan <rsneha(a)umd.edu<mailto:[email protected]>> wrote: I did another round of refinement with default settings (XYZ,realsp, IndB and occ) with and without weight optimization. Without weight opt, the Rfactors are 23/36 with RMSbonds-0.0108 and RMSangles-1.750 One idea would be to run AutoBuild again. I've seen cases before where it didn't converge using the default settings, and feeding a previous result back into the program for a second run produced significantly better models. It might help get rid of the overfitting. -Nat

5 12