- phenixbb - phenix-online.org

Install Phenix 2926 on Linux Fail
by Xiao Lei 18 Oct '17

18 Oct '17

Dear All, I was trying to install Phenix 2926 on Ubuntu Mate, after type sudo ./install I got the following fail message: ========================================================= Phenix Installation version: dev-2926 machine type: intel-linux-2.6-x86_64 OS version: 4.4.0-97-generic destination: /usr/local/phenix-dev-2926 # of processors: 4 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 275, in <module> installer(sys.argv[1:]).install() File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 197, in install self.install_from_binary() File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 319, in install_from_binary self.reconfigure(log=log) File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 379, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-dev-2926/base/bin/python /usr/local/phenix-dev-2926/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-dev-2926/build --command_version_suffix dev-2926 phenix phaser solve_resolve labelit dials xia2 iota prime' failed with exit code 1 What I need to do to fix this?

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SHELX sites to use in Phenix.
by Mahmudul Hasan 18 Oct '17

18 Oct '17

Dear All, I am trying to solve a structure using Phenix with very low anomalous signal. After several trials it seems like the signal from Manganese is not enough to solve this protein structure. Reading information that SHELX is good in finding sites from low molecular weight molecules (e.g. S, etc.), I tried the online version of SHELX in CCP4 to find the sites. Now I would like use these sites found by SHELX to see if that help to solve the structure. My question is, what is the best way to include extra sites besides the program Autosol find itself? Your valuable suggestions will help me a lot to get going with my structure solution effort. Best wishes, Mahmudul Lund Sweden

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Model_vs_data speed
by Eric Williams 16 Oct '17

16 Oct '17

I'm having a devil of a time getting model_vs_data to run in a timely fashion. Running the latest stable Linux build on Ubuntu 14.04 takes on the order of 3 minutes per structure. That wouldn't be so bad if I weren't trying to run it on every entry in the PDB. Is it just a limitation of Python? SFCheck, which I think is written mostly in FORTRAN, runs in a few seconds. Any help anyone could offer would be appreciated. Thanks. :) Eric

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Re: [phenixbb] Small change in molprobity report on output pdb between dev-2873 and dev-2919?
by Christopher Williams 09 Oct '17

09 Oct '17

I'll take a look. Thanks for noticing! -Christopher Williams ---Richardson Lab On Mon, Oct 9, 2017 at 12:44 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Boaz, > > I had to disable it because it required re-calculation of all other > Molprobity metrics twice, which it time waste. > > @developers: Can someone from Richardson Lab fix this? > > Pavel > > > > On 10/9/17 09:35, Boaz Shaanan wrote: > > Hi, > > I noticed a small change in output pdb between these two versions in the > molprobity report (these are two different runs, so ignore the numerical > values)t: > > *dev-2919:* > > REMARK 3 REMARK 3 > REMARK 3 MOLPROBITY STATISTICS. > REMARK 3 ALL-ATOM CLASHSCORE : 3.13 > RAMACHANDRAN PLOT: > REMARK 3 OUTLIERS : 0.46 % > REMARK 3 ALLOWED : 3.24 % > REMARK 3 FAVORED : 96.30 % > > *dev-2873:* > > REMARK 3 MOLPROBITY STATISTICS. > REMARK 3 ALL-ATOM CLASHSCORE : 2.56 > REMARK 3 MOLPROBITY SCORE : 1.24 This line is missing from the > newer version > REMARK 3 RAMACHANDRAN PLOT: > REMARK 3 OUTLIERS : 0.46 % > REMARK 3 ALLOWED : 2.78 % > REMARK 3 FAVORED : 96.76 % > > I am just wondering whether this change is intentional. > > Cheers, > > Boaz > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of Life > Sciences Ben-Gurion University of the > Negev Beer-Sheva > 84105 > Israel > E-mail: > bshaanan(a)bgu.ac.il <bshaanan(a)bgu.ac.il> Phone: 972-8-647-2220 Skype: > boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > > > _______________________________________________ > phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > >

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Rosetta installation
by Daniele de Sanctis 08 Oct '17

08 Oct '17

Hi all I have some trouble installing rosetta. I followed the instruction as in https://www.phenix-online.org/documentation/reference/rosetta_install.html and everything went ok up to % rosetta.build_phenix_interface nproc=n but then % rosetta.run_tests fails with Rosetta command-line arguments: -parser:protocol /buffer/desancti/xtal/rosetta_src_2016.32.58837_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s 1yjp_rosetta_in.pdb -mtzfile 1yjp_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1yjp_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -score:weights talaris2013_cart -nstruct 1 Generating 2 models on 1 processors... DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) Traceback (most recent call last): File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in <module> run(sys.argv[1:], create_dir=True) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs check_result(result) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Any idea? thanks Daniele

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Running Phaser with a already placed solution from a previous job
by vincent Chaptal 05 Oct '17

05 Oct '17

Dear everyone, this sounds trivial but I somehow can't make it work so I would appreciate any pointer. I have placed a component using phaser and would like to expand my search using this already placed component as partial solution. I open the full-featured interface of phaser in the GUI and select the box "Use partial solution from previous job" and select the job (nothing seems to happen there). I define my ensembles with ensemble_1 as "fixed partial solution" and ensemble_2 the one to search for. I then get the error message that "ense_1 from previous job is not specified on the current ensemble tab". Using the info button I see that "It is best to do this by modifying the configuration of the GUI from the previous Phaser run instead of starting from scratch, because the stored solutions do not contain the definitions of the search ensembles" but I don't understand what is asked for me to do here. When I restore the previous job, I can't see how I can start a new search from there. Any help would be greatly appreciated. Thanks Vincent I'm using phenix 1.12-2829. -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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map model correlations in real_space_refine
by Daniel Larsson 04 Oct '17

04 Oct '17

In version 1.12, what does the new map correlation numbers CC_mask, CC_volume and CC_peak in the log mean? How do they relate to the old "Map CC (whole unit cell)" and "Map CC (around atoms)" values (which in my opinion are more intuitive/descriptive and very useful numbers and I don't understand why they are no longer written to the log). Regards, Daniel

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help with phenix.ligand_identification
by Edward A. Berry 28 Sep '17

28 Sep '17

I'm having some problems using ligand_identification. I would like to restrict the search to a specific density peak, even if it is not the highest unmodeled peak or the highest Fo-Fc peak in the map. I tried using options: search_center="67.5 18.3 11.8" or ligand_near_res=S2063, Will the search be restricted to that region, or if a particuar ligand doesn't fit that blob, will it search through the rest of the map? If it is restricted, in what radius? Is this radius affected by the "search_dist" or "local_search" parameters? and local_search = True is default? Is there a threshold level for density level, below which building a ligand in a blob will not be attempted? I've tried with both search_center= and ligand_near_res=, and something gets built far away from that site. But there were errors, so I may have something wrong: phenix.ligand_identification mtz_in=sqr2803or13_031.mtz input_labels="2FOFCWT PH2FOFCWT" \ model=sqr2803or13_031.pdb ligand_near_res=S2063 nproc=2 After preparing the ligand library, then: Running LigandFit process 1... Number of atoms in ligand suc.pdb is 23 Running job sequence 1, ligand 2, in /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1... Evaluating all ligands in ligand-lib now...and placing fittedligand ### in resolve_ligand_###.pdb Number of atoms in ligand 2pe.pdb is 28 Running job sequence 0, ligand 1, in /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0... Process Process-2: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1382, in RunLigandFit shutil.rmtree(ligandfit_dir) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 247, in rmtree rmtree(fullname, ignore_errors, onerror) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 256, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 254, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1/LigandFit_run_1_/TEMP0' Process Process-1: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1382, in RunLigandFit shutil.rmtree(ligandfit_dir) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 247, in rmtree rmtree(fullname, ignore_errors, onerror) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 256, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 254, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0/LigandFit_run_1_/TEMP0' Evaluating LigandFit results ... The run continues, but it does not test any more ligands after those first two but goes on to evaluate the results. With nproc = 1, only 1 ligand gets tested. In all cases the first ligand in the library (2PE.pdb) is evaluated as the best. It is placed in density, but density that has already been built out with (and looks more like) a string of water molecules. And this is far from the selected residue or coordinates specified. The directory that raised the error when attempting to be deleted does eventually get removed: after the run there is no TEMP_N in the parent directory. Any suggestions would be welcome. Ed P.S. - running with .eff file: ['--show_defaults'] ligand_identification { mtz_in = sqr2803or13_031.mtz mtz_type = *F diffmap model = sqr2803or13_031.pdb ncpu = 1 n_indiv_tries_min = 30 n_indiv_tries_max = 300 n_group_search = 4 search_dist = 10 local_search = True search_center = "67.5 18.3 11.8" # ligand_near_res = S2063 verbose = False debug = False use_ligandfit = True search_mode = *default LigandFit temp_dir = Auto dry_run = False # number_of_ligands = 1 cc_min = 0.75 open_in_coot = False non_bonded = True keep_all_files = False # cif_def_file_list = real_space_target_weight = 10 # job_title = None ligandfit { } } gives: [['2pe.pdb', 'suc.pdb', . . . 'upl.pdb']] /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2 ******************************************************************************* Sorry, the protein model file None does not seem to exist? ******************************************************************************* Running LigandFit process 0... Process Process-1: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1122, in RunLigandFit shutil.copyfile(mtz_in,data_local) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No such file or directory: 'None' Evaluating LigandFit results ... Lig_seq Placed/total cc_all cc cc_adj score Code HBscore Cannot find overall_ligand_scores.log0. This could mean that none of that (sub)set of ligand fitted well. None of the ligand fit the difference desity well enough. Please try the following -- 1) if you input a custom library, try to use the default library (no extra keywords needed), or 2) if you used the default library already, ususlly this means that the density is too small (> 6 atome or more is needed.) Exiting ...... No good ligand found.

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"Headless" install
by Jared Sampson 25 Sep '17

25 Sep '17

Hi all - Is it possible to download and install the latest Phenix release to a node on a computing cluster (i.e. without a screen and therefore web browser)? I've tried pasting the latest download links into `curl` and `wget` commands but get zero-size files as a result. Thanks, Jared

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Deadline reminder: XChem fragment screening at Diamond (and iNEXT) - SUNDAY 1st OCTOBER
by Frank von Delft 23 Sep '17

23 Sep '17

Dear Protein Crystallographers and Drug Discoverers A reminder that we are again inviting proposals for performing crystal-based fragment screening at Diamond's XChem facility at beamline I04-1, for the next allocation period (April 2018 to Sept 2018). *The deadline for proposals is NEXT SUNDAY 1st OCTOBER 5PM.* *Details of how to submit at this page <http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening/Applying-for-Fragm…>. * Full details of the facility are available here <http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html>. It supports the full crystal-to-structure experiment, and since opening for users in 2015, it has hosted over 50 users from academia and industry, with over 65 experiments (>50k crystals) consistently yielding credible, high quality fragment hits. With the right crystals, it'll keep you busy for less than a few weeks; and you get lots of support and advice. The calls are heavily oversubscribed, so please pay close attention to the instructions and guidelines. Access for EU users is funded via iNEXT <http://www.inext-eu.org/> (but only if you follow the instructions!); however we welcome all international proposals. -- Prof Frank von Delft Associate Professor Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 Visiting Professor Department of Biochemistry University of Johannesburg South Africa

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refine error message
by Jiemin Zhao 22 Sep '17

22 Sep '17

Hi， I got an error message when I try to refine a molecular replacement result. It says "number of nonbonded interaction distances<0.001:10. Please inspect the out put above(or in the log window) and correct the input model file." Could you help me with this problem? The error happens when I add Mg to pdb file. Thanks! Best regards, Jiemin

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Weird occupancy values in HySS
by Dominic Gilzer 21 Sep '17

21 Sep '17

Dear everybody, I am using Phenix HySS to solve the substructure of an iodine soak. I tried several high resolution cut-offs and a varying amount of heavy atoms to search for, but consistently get occupancies of > 1.0. Has anyone noticed such values for occupancies before, and by chance knows how or why these occur? Best regards, Dominic

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refine error message
by Jiemin Zhao 18 Sep '17

18 Sep '17

Hi, I got an error message when I try to refine a molecular replacement result. It says Fatal problems interpreting model file: Number of atoms with unknown nonbonding energy type symbols: 18 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply-cif-modification and apply-cif-link parameter definitions if necessary. Could you help me with this problem? Thanks! Best regards, Jiemin

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Academic position in cryoEM at The University of York
by Jon Agirre 14 Sep '17

14 Sep '17

The Department of Chemistry at The University of York is seeking to make an appointment of a Lecturer/Senior Lecturer/Reader/Professor in the area of Cryo Electron Microscopy, the position being based in the world-renowned York Structural Biology Laboratory within the Department. The Department has been awarded >£2M by the Wellcome Trust and Wolfson Foundation to invest in state-of-the-art equipment and a bespoke building to house a modern 200 kV cryo-electron microscope, supported by significant investment from the University and a private donor. We are now seeking to appoint a high-calibre researcher in cryo-electron microscopy, with a clear vision to lead their own programme of excellent research within YSBL <https://www.york.ac.uk/chemistry/research/ysbl/>. Your research will complement the X-ray crystallography and NMR techniques currently used in the YSBL, and will bridge the gap between X-ray work and the optical microscopy in the Biology Technology Facility. The role is available at any level and we welcome interest from talented academics with an impressive research profile appropriate to the level of application and a collegiate approach to their work. You will be a dynamic research leader with a consistent track record in the application of cryo-electron microscopy to challenging biochemical/biological problems. We welcome applications from researchers with an interest in diverse areas of structural and cell biology, with particular interest in those working on mammalian systems. The Department of Chemistry is one of the UK's leading Chemistry departments and is renowned internationally for its research, having performed exceptionally strongly in the recent Nature Index 2017 Innovation Table <https://www.york.ac.uk/chemistry/news/deptnews/nature-index-2017-innovation…>. Combined with a commitment to high-quality teaching and outstanding student satisfaction, it is recognised consistently for its family-friendly policies and is proud of its Athena SWAN Gold Award. *Key requirements:* (viewed relative to the level of post applied for – see candidate briefs for more details) - PhD in Chemical, Biochemical or Physical Sciences - Specialist knowledge in cryo electron microscopy - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to define, lead, manage and attract funds for research, operating across disciplinary boundaries - Experience of and commitment to teaching and learning at undergraduate level. - Demonstrable capacity for creative thinking and planning - Substantial recent publication record in leading peer-reviewed journal - Evidence of national and/or international collaboration *Why York?* We are a dynamic, research-intensive university and have experienced significant growth over the past ten years, securing national and international recognition for our academic excellence. Our attractive, landscaped campus has seen significant development which will continue as the University continues to develop. Chemistry is a multidisciplinary department with an international reputation for excellence in research and teaching. www.york.ac.uk/chemistry *Salary will be commensurate with experience and grade* Lecturer: £38,832 to £47,722 Senior Lecturer: £49,149 to £56,950 Reader: £49,149 - £60,410 Professorial: current minimum £62,585 *To apply* Informal enquiries may be directed to Head of Department Professor Duncan Bruce (chem-hod(a)york.ac.uk; +44 (0)1904 322500) or the Academic Group Leader in YSBL Professor Tony Wilkinson (tony.wilkinson(a)york.ac.uk; +44 (0)1904 328261) Link: https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885&p_we… *Closing date:* 9 October 2017 *Interviews will be held in York on:* 29 November 2017 -- Dr Jon Agirre Royal Society University Research Fellow York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, UK http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Office: /B/K/065 Phone: +44 (0) 1904 32 8270 Twitter: @alwaysonthejazz

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Macromolecular Crystallography workshop in South America
by Felipe 12 Sep '17

12 Sep '17

Dear colleagues, We are pleased to announce our sixth edition of the Workshop: Macromolecular Crystallography School "From data processing to structure refinement and beyond", to be held at the Institut Pasteur de Montevideo (Uruguay). This Workshop will cover all aspects of the macromolecular structure determination process using X ray crystallography: starting from data processing, through phasing and refinement to structure completion and analysis. Integrative methods are also being included. In particular, this year an introduction to cryo-electron microscopy has been added to the program. http://pasteur.uy/mx2017 <http://pasteur.uy/mx2017> Dates: November 13 - 23, 2017 Confirmed speakers and tutors: Alejandro Buschiazzo, Montevideo, Uruguay Grzegorz Chojnowski, Hamburg, Germany Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil James Holton, San Francisco/Berkeley/Palo Alto, USA Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge, UK Garib Murshudov, Cambridge, UK Colin Palmer, Oxford, UK James Parkhurst, Oxford, UK Randy Read, Cambridge, UK Clemens Vonrhein, Cambridge, UK Please find the program of the Workshop, the application form and further contact information, at http://pasteur.uy/mx2017 <http://pasteur.uy/mx2017> This Workshop is supported by the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de Biologia Estructural del Mercosur (CeBEM); the International Union of Crystallography (IUCr); and the Institut Pasteur de Montevideo. Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil Applicants: 24 students will be selected, aiming at advanced PhD, postdocs and young researchers. The Course will provide financial support covering registration fees, and for the case of those students coming from abroad, all local expenses (lodging, per diem and local transportation). Look in the www site for details on application procedures. The application deadline is September 17, 2017. Please address further inquiries to: mx2017(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! Felipe Trajtenberg, PhD Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 143 Fax: +598 25224185 http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular… <http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular…>

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Gold atoms in cryo-EM
by a.malay＠riken.jp 12 Sep '17

12 Sep '17

Dear all, I hope that this question is neither too off-topic or naive. I am trying to refine a large protein structure against a cryo-EM map using Phenix real-space refinement. The protein complex is unusual in that the oligomeric state is held together via coordinated gold atoms. However, there seems to be a problem with refinement, in that the the gold atoms show extremely high B-factors (>200) after refinement, whereas the B-factors of the protein residues, including those surrounding the gold atoms, adopt more reasonable values. My question is: could the unusually high B-factors of the gold atoms be somehow due to differences in the relative scattering of Au atoms when obtained from X-ray vs. electron beam irradiation? And if so, is there any way to correct for this? Thank you in advance for your kind help. Best, Ali

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SLURM Batch submission
by Heidi Schubert 11 Sep '17

11 Sep '17

Hi Has anyone successful submitted phenix jobs to a SLURM batch queue? I guess, in theory, I did successfully submit a job but it took a while to start and after completion the log files did not successfully link back to the interface losing the graphic feedback. I can’t tell how the job was submitted. Our submission command is sbatch, which is what I put in the Phenix Preference > Processes queue command. But locally we have a header on our sbatch submission which spells out our wall time, account and MPI expectations/requests. Is there an environment file that Phenix reads to provide this information or does it submit generically? I wondered if this was responsible for the long delay of the start of our job (sure – could have been a busy queue). Anyone know how to get the GUI to read the output files when it loses connection to the run? Heidi

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Resolution of datasets for using PHENIX automated ligand identification
by Xiao Lei 01 Sep '17

01 Sep '17

Hi All, I am asking is there any resolution requirement for using the PHENIX automated ligand identification tool. Can I use the tool with 3A resolution protein datasets?

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.hhr files?
by Patrick Loll 01 Sep '17

01 Sep '17

This feels like a silly question, but I’ve already wasted some time head-banging, so here goes: I would like to generate a .hhr sequence alignment file for use in MR-Rosetta. After running HHPRED, I get a lovely alignment, but I see no place to save it as a .hhr file. Several “how-to” pages talk about a “save” button above the alignment, but the MPI bioinformatics pages seem to have been reformatted in the past few months, and I see no such button. There is a tab labeled “raw output” with a download option, but that appears to give a FASTA format. So…can anyone suggest a way forward? Either by capturing the elusive .hhr file, or by saving the data in some other format that is still useful for MR-Rosetta? Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjloll(a)gmail.com pjl28(a)drexel.edu

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Few questions about the model building and refinement of cryo-EM data
by Wang, Bing 28 Aug '17

28 Aug '17

Hi guys, Sorry for the detailed questions from a beginner! I am starting a modeling/refinement work for a set of cryo-EM data. Data basic information: phage data (looks like a ball with P1 space group), map size ~870 MB, resolution ~6 A, two X-ray structures for model building General strategies: I select COOT for the model building; using phenix.real_sapce_refine for the real space refinement with secondary structure restrain and REFMAC for the reciprocal space refinement. Few questions are listed here. 1. The map was too bigger to open it in COOT. The phenix.map_to_structure_factors was used to obtaine ~120 MB sized MTZ file (still a little big for my computer). I manually build up the whole ball-shaped phage with the rigid body fit in COOT (from two X-ray structures to 120 chains). My first question will be: In this case, should I crop the map in Chimera or other software and only focus on a small asymmetric unit to do the model building and the followed refinement. 2. I would like to do a real space refinement after the model building. Input files: A pdb file I just built up from COOT A original MAP file A transfered MTZ file Two restraint files from two X-ray structures by ProSMART (TXT formart) The refinement parameters I would like to select in GUI interface: minimization_global, rigid_body, local_grid_search, adp Use secondary structure restraints Reference model restraints: use starting model as reference, main chain, side chain, fix outliers, secondary structure only Rotamer restraints Ramachandran restraints Show per residue My second set of questions: Should I select the MAP file (~870 MB) or the MTZ file (~120 MB)? Is that necessary to add the two restraint files from ProSMART if I use the starting model as reference? Is the refinement parameters selected properly? 3. I gave a try by phenix.real_space_refine. An first error showed up: Number of atoms with unknown nonbonded energy type symbols: 6840 "ATOM 184 HG1 SER 1 12 .*. H " "ATOM 458 HG1 SER 1 30 .*. H " "ATOM 699 HG1 SER 1 45 .*. H " "ATOM 720 HG1 SER 1 47 .*. H " "ATOM 762 HG1 SER 1 50 .*. H " "ATOM 1241 HG1 SER 1 81 .*. H " "ATOM 1465 HG1 SER 1 95 .*. H " "ATOM 1747 HG1 SER 1 113 .*. H " "ATOM 1758 HG1 SER 1 114 .*. H " "ATOM 2173 HG1 SER 1 141 .*. H " ... (remaining 6830 not shown) I tried phenix.ready_set to fix this problem according to a previous discussion but it gave me another error: ENDMDL record missing at end of input. Thus my third question will be how to fix the first error? Thank you for patience! I would really appreciate your help! Bing

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Opening phenix X-ray/neutron maps in Coot without the Phenix GUI
by Derek Logan 23 Aug '17

23 Aug '17

Hi ccp4bb and phenixbb, Is there a convenient way to open MTZ files in Coot that are the result of joint X-ray/neutron refinement in phenix.refine, but where phenix.refine was run in command-line mode? I would like achieve what is done in the Phenix GUI at the click of a button, i.e. open Coot with the structure and 2Fo-Fc and Fo-Fc maps for both neutron and X-ray. At the moment I have to open each MTZ file four times in the Coot GUI, once for each type of map. Is there a script buried somewhere in the Phenix installation that can be modified? /Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science bit.ly/2d0HxmS Lund University, Box 124, 221 00 Lund, Sweden

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Master Your Proteins, NKI Amsterdam, 20-23 November 2017
by Anastassis Perrakis 18 Aug '17

18 Aug '17

Dear all, Applications for the Instruct-ERIC course on Biophysical Characterisation of Macromolecules and Quantification of Biomolecular Interactions are now open. The course aims to provide the theoretical background of popular biophysical methods that are often used in relation to Structural Biology research, and practical experience both in performing experiments and in analysing the resulting data. The rationale behind an extended kit of experiments to characterise macromolecules and their interactions will be explained. You will be shown how to perform and analyse the related experiments in dedicated practical sessions. The course will include theory and practical sessions on thermal shift assays (also label free), Surface Plasmon Resonance, sothermal Titration Calorimetry, Miscroscale Thermophoresis , Fluoresence Methods, Stopped Flow, and the Graphpad/Prism and Kintek analysis software. Details can be found at: https://www.structuralbiology.eu/events/biophysical-characterisation-of-mac… <https://www.structuralbiology.eu/events/biophysical-characterisation-of-mac…> On the behalf of the organisers, Tassos

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Macromolecular Crystallography workshop in South America
by Alejandro Buschiazzo 17 Aug '17

17 Aug '17

Dear colleagues, We are pleased to announce our sixth edition of the Workshop: Macromolecular Crystallography School "From data processing to structure refinement and beyond", to be held at the Institut Pasteur de Montevideo (Uruguay). http://pasteur.uy/mx2017 Dates: November 13 - 23, 2017 Confirmed speakers and tutors (so far... a few more may join the crew): Alejandro Buschiazzo, Montevideo, Uruguay Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge, UK Garib Murshudov, Cambridge, UK Colin Palmer, Oxford, UK James Parkhurst, Oxford, UK Randy Read, Cambridge, UK Clemens Vonrhein, Cambridge, UK Please find the program of the Workshop, the application form and further contact information, at http://pasteur.uy/mx2017 (this www site will be updated regularly, so stay tuned!) This Workshop is supported by the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de Biologia Estructural del Mercosur (CeBEM); the International Union of Crystallography (IUCr); and the Institut Pasteur de Montevideo. Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil Applicants: 24 students will be selected, aiming at advanced PhD, postdocs and young researchers. The Course will provide financial support covering registration fees, and for the case of those students coming from abroad, all local expenses (lodging, per diem and local transportation). Look in the www site for details on application procedures. The application deadline is September 17, 2017. Please address further inquiries to: mx2017(a)pasteur.edu.uy Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Associate Professor Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular…

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Postdoctoral position at the University of Chicago
by Robert Keenan 15 Aug '17

15 Aug '17

The Keenan lab at the University of Chicago has an opening for a postdoctoral scientist to study the structure and function of protein complexes involved in membrane protein biogenesis and quality control. Applicants should be nearing completion of a PhD in structural biology and have a strong academic record with significant publications. Experience in molecular biology, protein purification and electron microscopy/x-ray crystallography is required. To apply, please send a CV and a short statement describing your motivation for wanting to join the lab. Please be prepared to arrange for three letters of reference to be sent by email. For more information, please visit our webpage: http://keenanlab.bsd.uchicago.edu

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Phenix.real_space_refine
by Reza Khayat 11 Aug '17

11 Aug '17

Hi, I am refining a virus into an image reconstruction and have been having issues using the NCS capability of phenix.real_space_refine_1.12-2829. I think it may be my misunderstanding of the manual. The virus has 60subunits and I am feeding phenix a complete oligomer. I manually modify the first subunit with coot (simple movements and such), define an NCS group file where the first subunit is the reference and the other 59 are selection, and feed these into phenix.real_space_refine. Does phenix recapitulate my modifications of the first subunit into the remaining 59 subunits to create an oligomer that contains all my modifications before starting refinement? Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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Appplying symmetry to a Cryo-EM map in phenix map_to _model
by Joshua Jude Lobo 11 Aug '17

11 Aug '17

Hi Phenix Group I am very new to model building and using phenix . I am trying to use phenix.map_to_model to generate a model just using my cryo-EM map( mrc format) and a fasta sequence .My protein has octahedral symmetry . I found the use_space_group_symmetry argument but am not sure what argument to give to impose the symmetry . Any inputs are appreciated Sincerely Joshua Lobo University of Minnesota Twin Cities

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seeking advice on how to configure Phaser-MR (full-featured) to use a previous partial solution
by Emilia C. Arturo (Emily) 08 Aug '17

08 Aug '17

Hello. I have a 3-domain protein (let's say it's organized from N to C as A-B-C) whose structure I am working to determine now. Although several single- (A alone, B alone), double- (A+B and B+C) and 3-domain (A+B+C) structures of this protein (from a different organism whose primary sequence is, overall, ~85% identical to the one on which I'm working) have already been determined and deposited in the PDB, I would ideally like to use a minimal probe (i.e. as few domains as possible) in order avoid model bias that could be imposed on the relative orientation of domains A, B, and C. So far, I have phase solutions (TFZ scores for all in the high-50s and 60s) using B-only, A+B, and B+C pdb files as probes. A-only structures have not given a phase solution (TFZ is ~7 and autobuild gives a solution that looks unbelievable in Coot), perhaps because A is relatively small in size. Here is my problem: I suspect that A and B sit relative to one another in an interesting way in this particular structure, so I'd like to use Phaser to search for a solution given the fixed partial solution from a B-only search, together with an A-only structure as a separate probe. So far no MR solutions have been found when I configure the run with an A-only pdb file and a B-only-derived Phaser result that is input as a fixed partial solution. I'm writing to ask for advice on how to configure the search. I think that the problem is my configuring the search, and not that a solution cannot be found from these coordinates. This is the reason I think that my problem is in configuring the search; please correct me if I'm wrong: Using a Phaser result derived from using an A+B structure as probe, I cut up the resulting pdb file into 2 pdb files - one containing an A' and another containing a B', where A' is the A domain of the Phaser result, and B' is the B-only part. Then I configured a Phaser result with B' as an ensemble that is a fixed partial solution, and A' as a separate ensemble/probe. I searched for 4 of each since 4 chains is the most likely composition in the ASU. I expected to get a result similar to what Phaser calculated when I input the A+B structure as an intact probe. Instead of getting a solution where 4 A+B chains were placed as they were in the first Phaser result, which gave one solution with a TFZ score of 65, I got 13 solutions, the top scoring a TFZ of 7.5, and each solution having a total of 9 chains - 4 As and 5 Bs. Is anyone willing to help me troubleshoot the above before I throw up my hands and settle on either manually building two domains onto the single-domain solution, or one domain onto the 2-domain solution, keeping in mind the potential for model bias? I am keen on using the B-only solution as a fixed partial solution to place domain A because all the B-only structures provide coordinate information for a portion of domain B that is unresolved in any of the multi-domain structures that contain domain B. I am using the Phenix gui, version 1.12rc1-2807. Regards, Emily. -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott

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Very low rmsd bond length
by Mark Saper 07 Aug '17

07 Aug '17

Hi all, A reviewer points out that my refined structures (which have already been deposited in PDB) have very small RMSD values for bond lengths (0.005–0.002) (refinement resolutions are 2.0–2.8 Å), and that my weights should be decreased. The weights were calculated with “Optimize XYZ Weight” option turned ON. This seems to be the case with all of the structures that I have refined during the past 5 years. My impression from previous discussions is that deriving explicit weights from these optimized ones is not straightforward and so I have never tried to relax the weights. Moreover inspecting the optimization results in the log file, suggest that changing the weights to increase the RMSD would increase the Rfree. (I can post this if its helpful). How do I address the reviewer’s concerns? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

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Comput. Cryst. Newsl. (2017) 2
by Nigel Moriarty 05 Aug '17

05 Aug '17

The latest Computational Crystallography Newsletter is available for download. Below is the clickable table of contents. July 2017 <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf> Short Communications - phenix.mtriage: a tool for analysis and validation of cryo-EM 3D reconstructions <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf#page=6> - More TLS validation with phenix.tls_analysis <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf#page=8> Fitting tips #14 – How Ser & Thr behave oddly on helices <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf#page=2> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging 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

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mrc to mtz conversion to open map in coot
by Joshua Jude Lobo 03 Aug '17

03 Aug '17

Hi phenixbb I am new to phenix and am trying to convert a cryo-em map(mrc format) to mtz format using the phenix.map_to_structure_factors command .This proceess finishes without errors but the resultant mtz file is not viewable in coot . I have tried both the phenix.map_to_model and the phenix.map_to_model_histogram_1.12-2829 How is the best way to troubleshoot this ? Any inputs would be appreciated Sincerely Joshua Lobo University of Minnesota Twin Cities

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Berkeley servers are back in service
by Billy Poon 03 Aug '17

03 Aug '17

Hi everybody, The servers at Berkeley are now available. Please let us know of any issues. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Lab Evac
by Nigel Moriarty 03 Aug '17

03 Aug '17

Folks The Grizzly Fire (the media loves a interesting name) is more than 50% contained and the lab is now open. The servers are, once again, available for downloading the latest version of Phenix, 1.12. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging 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

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Emergency shutdown
by Nigel Moriarty 02 Aug '17

02 Aug '17

Folks Phenix servers are shutting down due to a grass fire in the area. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging 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

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Postdoctoral position in Structure and Function of Fungal Membrane Proteins
by Maike Bublitz 02 Aug '17

02 Aug '17

Postdoctoral position in Structure and Function of Fungal Membrane Proteins A post-doctoral position is available in the research group of Associate Prof. Maike Bublitz at the Department of Biochemistry, University of Oxford. The project aims to understand the structure and function of fungal membrane transport proteins identified as potential new drug targets, using a combination of state-of-the-art structural (X-ray crystallography, cryo-EM) and biochemical/biophysical techniques. Applicants should hold a PhD in a relevant subject area, such as membrane protein biochemistry or structural biology. Experience in native or recombinant membrane protein expression, purification and either structural determination or functional analysis using biochemical and biophysical techniques is essential. Ability to work in a team as well as contribute to supervision activities and excellent verbal and written communication skills are expected. Experience in protein X-ray crystallography and/or cryo-EM is an advantage. To apply for this role and for further details, including the job description and selection criteria, please click on the link below: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Applications for this vacancy are to be made online by 31th August 2017.

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(no subject)
by Priyanka Abeyrathne 21 Jul '17

21 Jul '17

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Phenix version 1.12 released
by Paul Adams 14 Jul '17

14 Jul '17

The Phenix developers are pleased to announce that version 1.12 of Phenix is now available (build 1.12-2829). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights for this version: New tools for secondary structure validation, comparing multiple related structures, cryo-EM model and map validation, and calculation of real space difference maps. Video tutorials are now available on the new Phenix Tutorial YouTube channel (www.youtube.com/c/phenixtutorials). A suite of tools for cryo-EM model building and structure refinement including automated map sharpening, segmentation, and model building. Real space refinement now has an option to use histogram equalized map as a refinement target. Phaser version 2.8 has several new features, including unit cell refinement for EM data, more extensive use of eLLG in decision making and analysis, anomalous substructure determination (Phassade), improved tNCS detection and analysis, and improvements to SCEDS. - NEW TOOLS - phenix.secondary_structure_validation - tool to validate secondary structure section in .pdb and .mmcif files with option to filter bad annotations. - Structure Comparison: tool for parallel validation and analysis of near-identical protein structures. Results include the analysis of ligands, rotamers, Ramachandran angles, missing atoms, water locations and B-factors. - phenix.mtriage: command-line tool to validate cryo-EM models. GUI is available. Computes various map statistics including resolution estimates, FSC between half-maps, full and model maps. Outputs mask file used to compute FSC. Still under development. - phenix.real_space_diff_map: command-line tool to compute difference map. This is a real-space analogue of Fo-Fc map mainly designed for cryo-EM maps. See http://phenix-online.org/newsletter/CCN_2017_01.pdf for details. - PHENIX VIDEO TUTORIALS Video tutorials about Phenix tools are now available on the Phenix Tutorial YouTube channel (www.youtube.com/c/phenixtutorials). The following topics are covered: - How to run phenix.refine - How to calculate polder maps - How to run phenix.real_space_refine - How to run PDB tools - How to change phenix.refine parameters via the GUI - Basic Phenix eLBOW tutorial - How to run Phaser-MR from the Phenix GUI - Explaining the atom selection syntax - How to run Structure Comparison - NEW FEATURES - Phenix.auto_sharpen: New map sharpening algorithms available based on (1) optimization of map clarity (adjusted surface area or kurtosis), (2) resolution-dependent map-model correlation, (3) resolution-dependent half-map correlation, and (4) local map sharpening - Phenix.map_to_model: Iterative map improvement using model from one cycle to optimize sharpening of the map for the next cycle - Phenix.map_to_object: Now you can individually map each member of a group of chains onto your target - Phenix.chain_comparison: Now can compare a target to each of a group of models - Phenix.find_alt_orig_sym_mate: Now uses ssmalignment.stats to see what residue pairs were included by ssm in a hypothetical calculation of the ssm-rmsd. This is to avoid including atoms that even for an optimal structural alignmentwould have been too far apart that ssm would use them. Excluding these is necessary to avoid having the calculated rmsd blow up. - Now using angles for restraining hydrogen bonds in alpha helices and beta sheets in secondary structure restraints. - Phenix.polder: New option (compute_box=True) to compute a difference map excluding the bulk solvent mask within a user-defined box. The map can be used to inspect interesting difference density peaks. - phenix.map_model_cc (phenix.model_map_cc): various enhancements and bug fixes. - phenix.real_space_refine: - improved ADP refinement (still group) - improved NCS constraints definition - multi-model PDB file is not output by default anymore - (experimental) option to use masked histogram equalized map as refinement target. Using such map dramatically improves refined model geometry. This map is not suitable for ADP refinement. - show CCmask, CCvolume and CCpeaks that report on local and gloabal model to map fit. - RESTRAINTS - Specialised restraints for ligands with differing chemistry in the same model allows using the same 3-letter code but different restraints for a specific instance - apply_cif_restraints - Detailed control of peptide planes and omega angles - apply_all_trans - apply_peptide_plane - apply_cis_trans_specification: use an atom selection (CA) to force a cis or trans omega angle - REEL - Improvements to robustness and features - GUI - New interfaces - phenix.mtriage - phenix.map_box - phenix.auto_sharpen - phenix.map_to_model - phenix.ncs_average (under "Other Tools") - phenix.sculpt_ensemble (alpha) - Updated interfaces - Comprehensive Validation shows real-space correlations from phenix.map_model_cc when map files are used - Structure Comparison - Validation - improved speed of clashscore validation - bug fix to handling of cis-peptides in ramalyze - contours for ramalyze, rotalyze, and cablam now accessible at https://github.com/rlabduke/reference_data - validation GUI now shows altloc identifirs for most outliers - improved internal code accessibility of validation statistics - Phaser-2.8.0 - refinement of cell for data (electron micrcoscopy) - more analysis using eLLG for component addition - more analysis using eLLG for polyalanine residues for target eLLG given rms - more analysis using eLLG for single atoms more ordered than average - more analysis using eLLG for chains/gyre-and-gimble * Phassade: Fast Fourier Transform Anomalous Substructure Determination - SOLU TRIAL records RF-LLG for trial orientation - gyre and translation function report RF recorded for trial orientations - 'scons --ccp4' command line flag for ccp4 build (generates ccp4-style headers) * improved tNCS detection and analysis * gyre and gimble improved for output and python scripting * NMA outputs all perturbed files in MODEL delimited pdb file '<fileroot>.nma.pdb' * sceds outputs domains to chain delimited file '<fileroot>.nma.pdb' - sceds domain pdb file have TER separated domains - NMA option to output separate pdb files for each perturbation (XYZOUT NMA ALL OFF) - sceds option to output separate pdb files for each domain (XYZOUT NMA ALL OFF) - NMA has option to turn off output of input coordinates (NMA ORIG ON) - pdb chain identifies can be left unchanged from input (XYZOUT CHAIN COPY) (for Eleanor) - bugfixes -- allow peaks and purge percent to override one another if not default -- rms estimation developer options not being set correctly -- throw out of memory error if Patterson map allocation fails 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 Division Director, Molecular Biophysics & Integrated Bioimaging, 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 33, Room 347 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 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Problem with smiles string in elbow
by Edward A. Berry 13 Jul '17

13 Jul '17

I'm not getting the expected result with this string: COC(=O)C(=COC)c1ccccc1COC(N1C)=CC(=N1)C(=C2O)C=C(Cl)C=C2 When used with coot Lidia it gives the expected result (upper picture). But when I run elbow like this: phenix.elbow --smiles="COC(=O)C(=COC)c1ccccc1COC(N1C)=CC(=N1)C(=C2O)C=C(Cl)C=C2" --output="Y7303" --id="Y03" the result is the lower picture. In particular the pyrazole ring (arrow) gets distorted, but other bond lengths are way off. I want to use elbow because it names the atoms as numbered in the order they appear in the smiles string, irrespective of the element. This is good because this is one of a series of compounds in some of which C's are replaced by N's and vice versa so it helps to have the same number for atoms in the same position. What does work is to save the structure as .mol from Lidia and feed that to elbow, which gives the right structure and the elbow atom names. But it would be good to find out why it isn't working directly. my elbow is: electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.12rc1-2801 None

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Problem with rotamer refinement
by Renato Ferras 11 Jul '17

11 Jul '17

Dear all, I am refining a protein structure at 1.74 A resolution with phenix.refine (version 1.10.1_2155) and I have noticed that some side chains don't remain in the electronic density even after careful hand adjustment in which they are almost perfect. It seems pretty clear where the side chain should (must) be located, moreover it is consistent with two rotamers (either rotamer tp60 - #4 in coot - or rotamer tp-100 - #9 in coot -, which are approx. at 180 deg for chi3). In spite of that, after reciprocal space refinement, I observe that the end of side chain rotates chi3 angle and both N and O gets far from where they started (there is this difference in the chi3 angle). My concerns are about the proper interpretation of geometrical restraints listed in .geo file, specially what the ideal value is, how weights are applied to ideal value and why phenix doesn't reach convergence in reciprocal space refinement. Below are the values from .geo for the referred Gln: dihedral pdb=" CB GLN B 21 " pdb=" CG GLN B 21 " pdb=" CD GLN B 21 " pdb=" OE1 GLN B 21 " ideal model delta sinusoidal sigma weight residual 0.00 23.41 -23.41 2 3.00e+01 1.11e-03 8.42e-01 is there a description for us to interpret what these numbers are? To my understanding, the ideal values are established as being either 0 or 180 degrees (yet sinusoidal 2). I cannot say about how heavy the weights are on these (in fact, I left my refinement to optimize weights), but anyway, if I understand correctly, the ideal value (for chi3) should be rotamer dependent. Taking Gln as an example, I see several rotamers do have values close to either 0 or 180 degree, but what about rotamers 4 and 9? I might imagine a similar situation for residues like Asn and His, though I have not searched deep for these yet. Thanks, Renato

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crystal imaging system
by Sebastiano Pasqualato 30 Jun '17

30 Jun '17

Dear all, we are in the process of considering the purchase of a new Crystal Imager. So far, we have been considering the Formulatrix Rock Imager 182 and the TriTek Crystal Pro HT. I would be extremely grateful to anyone who could provide me: - feedback and user experience (positive/negative) on those instruments; - information on other instruments you would suggest. Thank you very much in advance, wishing you a pleasant weekend, best regards, ciao, 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/IEOXtalUnit

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Phenix polder error
by Avinash Punekar 26 Jun '17

26 Jun '17

Dear all, When I run phenix.polder through command line, I get a message "Sorry: Multiple equally suitable arrays of observed xray data found." and phenix.polder stops without producing the maps. How to solve this problem? Any help is highly appreciated. Thanks, Avinash

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does phenix refine fill in missing data?
by Ursula Schulze-Gahmen 22 Jun '17

22 Jun '17

I have very anisotropic data. I used the staraniso webserver to analyse and process my data which creates a final merged file with very incomplete data in the outer shells. If I use this data file in Phenix, what will happen? Will Phenix automatically fill in the unobserved data? If so, can I prevent it from doing so? I am importing the data with the reflection file editor and it seems the reflections are being filled in already at this stage. Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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Cif file recognition
by Joel Tyndall 22 Jun '17

22 Jun '17

Hi there, Having a few minor issues with my phenix setup on windows 10. I have the latest stable build Phenix1.11.1-2575. When introducing a new ligand that exists in the monomer library, Pheix complains it does not have the geometry restraints (cif file) - somehow it is not seeing its own library. How can I set up the cif library as default? Cheers Joel Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | Te Kura Mātauraka Wai-whakaora University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Skype: jtyndall Website | pharmacy.otago.ac.nz

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sculptor modifications
by Emilia C. Arturo (Emily) 21 Jun '17

21 Jun '17

Hello All, Is there a way to identify quickly the changes to a model that Sculptor has made? I am running the Phenix GUI to use Sculptor. I have read through the out-put log file, and understand (mostly) the sculpt protocol as it relates to the circumstances under which modifications to main chain or side chains are made, but it would be nice to see (in a list format, perhaps) what changes (if any...) were made. Regards, Emily. -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott

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phenix.map_to_model input mtz file failure
by dancingdream＠163.com 19 Jun '17

19 Jun '17

Dear Phenix bb, I intend to build a initial model by phenix.map_to_model. And the command line is as follows: phenix.map_to_model_1.12rc0-2787 map_coeffs_file=../rep_dm.mtz map_coeffs_labels="'FP,SIGFP' 'PHIDM' 'FOMDM'" seq_file=../resolve.seq is_crystal=True use_sg_symmetry=True density_select=False truncate_at_d_min=True and the feedback like this: Sorry: No initial assignment made for map_coeffs. Labels used: FP,SIGFP PHIDM FOMDM. Available labels: ['PHIB', 'FOM', 'HLA,HLB,HLC,HLD', 'FP,SIGFP', 'PHIDM', 'FOMDM', 'FDM', 'HLADM,HLBDM,HLCDM,HLDDM'] NOTE: grouped labels like 'FP,SIGFP' must stay together, have commas, and have no spaces. If they come from an MTZ file, they must be in adjacent columns as well. Suggested labels to use: PHIDM FOMDM I try many other input format of map_coeffs_labels, such as map_coeffs_labels="FP,SIGFP PHIDM FOMDM" map_coeffs_labels=["FP,SIGFP PHIDM FOMDM"] ... ... but the result is the same. Dose anyone can tell me how to fix this problem? Thank a lot. -- Wei Ding P.O.Box 603 The Institute of Physics,Chinese Academy of Sciences Beijing,China 100190 Tel: +86-10-82649083 E-mail: dingwei(a)iphy.ac.cn

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Overall anisotropic ADP in phenix.real_space_refine?
by Oliver Clarke 17 Jun '17

17 Jun '17

Hi, I wonder in phenix.real_space_refine whether it may be worth adding refinement of a single overall anisotropic ADP to the model - or a single TLS group with modeled anisotropic ADPs - in order to model the effects of overall orientation errors (which affect resolution more substantially towards the periphery) and preferred orientation (which tends to give rise to anisotropic resolution across the volume). Maybe this would be helpful at least in generating a calculated map that is better for difference map calculation, for example? Cheers Oli

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real_space_refine questions
by Daniel Larsson 14 Jun '17

14 Jun '17

I'm have some questions about doing real space refinements using phenix.real_space_refine. I am refining a model for an intermediate-resolution (3.79 Å) cryo-EM map. As the starting point I use a model from a higher-resolution map (3.25 Å) of the same system in another conformation. My idea is to first do rigid body fitting of domains and then gradually relax constrains and restraints. - Is it possible to restrain the position of certain parts of the model (i.e. "freeze" them so that they move at all) to do focused refinement of subdomains or loops? - In the instructions it says that you can do both NCS constraints and restraints. How you do the latter? I can only do the former by default or by defining ncs_constraints=True and give a NCS definition file. - When I do a run with run=rigid_body, some rigid body groups move in to each other and overlap. Is there no collision detection using this algorithm? If I do a run=minimization_global, things work a bit better in this regard, but is not really what I want (at this stage). Am I doing something wrong? Here is the run command and the rigid body definition file: phenix.real_space_refine \ model.pdb \ map.ccp4 \ rigid.eff \ resolution=8.0 \ ncs_constraints=False \ rotamer_restraints=True \ ramachandran_restraints=True \ c_beta_restraints=True \ run=rigid_body \ macro_cycles=10 # rigid.eff: refinement { rigid_body { group = chain A and resseq 101:266 group = chain A and resseq 273:388 group = chain B and resseq 101:266 group = chain B and resseq 273:388 group = chain C and resseq 104:266 group = chain C and resseq 273:388 } } Regards, Daniel Larsson

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 13 Jun '17

13 Jun '17

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the July 2017 issue is 30 June 2017. 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 33R0349, Molecular Biophysics and Integrated Bioimaging 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

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preparing DL-Malic acid stock solution
by Sebastiano Pasqualato 08 Jun '17

08 Jun '17

Dear all, we’ve recently having trouble preparing a 3 M stock solution of DL-Malic Acid, pH 7 (which we had, so it’s doable!). When we reach pH 3 - 4 the solution turns milky white and does not goes back to a clear solution even when the pH is raised. Does anybody have any advice on how to get a clear solution? Has anyone gone through the same? Thanks in advance, ciao, Sebastiano -- 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/IEOXtalUnit

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Re: [phenixbb] AutoSol invalid MTZ column_types error
by Terwilliger, Thomas Charles 08 Jun '17

08 Jun '17

Hi Mintu, I'm sorry about this problem! I should have fixed it already but missed this message from Phil Evans that he posted in January: "Columns N(+) and N(-), both of type I, are recent additions to the output file from Aimless. They are the number of observations merged into I(+) and I(-) respectively" AutoSol doesn't know about these columns and can accidentally guess that they are data. To get around this column, use a command like this to create a data file that does not contain the N(+) and N(-) columns: phenix.reflection_file_converter aimless.mtz --mtz=aimless_noN.mtz --label="I(+" ?where the --label=xxxx command specifies the first few characters of the columns you want to use as I+/I- data. Then use aimless_nonN.mtz instead of aimless.mtz as input to autosol. I will fix this in autosol. Let me know if that does not do it! All the best, Tom T Dear all, I am getting an error message "Invalid MTZ column_types for the given miller_array." while I try to run AutoSol. The last line in the log is "Adding array ['N(+)', 'N(-)'] to output file with type II". Do you have any suggestion how to fix this error? Thanks a lot in advance. Best, Mintu

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comfortable OS X level
by Patrick Loll 07 Jun '17

07 Jun '17

I’m still running Yosemite on my Macs, both because I’m change-averse and because folks reported problems with some crystallographic software upon upgrading the OS. These reports have now faded into the haze of the past, and so I ask, have the issues been resolved? Is it safe to move to Sierra? Thanks as always, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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