- phenixbb - phenix-online.org

Why can't I use bootstrap.py in cctbx to compile phenix?
by Taimin Yang 17 Nov '16

17 Nov '16

Dear Professor, My name is Taimin Yang and I am a PhD student in Stockholm University. I try to compile my own phenix using bootstrap.py but here is the error information: root@Linux-main:/usr/local/crystallography_software/phenix# python bootstrap.py --builder=phenix --with-python=/usr/local/anaconda2/bin/python hot update build Performing actions: hot update build Traceback (most recent call last): File "bootstrap.py", line 2034, in <module> run() File "bootstrap.py", line 2029, in run enable_shared=options.enable_shared, File "bootstrap.py", line 926, in __init__ map(self.add_module, self.get_codebases()) File "bootstrap.py", line 1051, in add_module action = MODULES.get_module(module)().get_url(auth=self.get_auth()) File "bootstrap.py", line 553, in get_url raise Exception('No anonymous access method defined for module: %s. Try with --%s'%(self.module, e.args[0])) Exception: No anonymous access method defined for module: chem_data. Try with --cciuser What should I do to compile my own phenix? Thank you very much. Best regards, Taimin

3 3

Failed to refine B factors of some residues and ligands
by Zhou, Tongqing (NIH/VRC) [E] 16 Nov '16

16 Nov '16

Dear All, I am refining a structure with diffraction to 2.2A resolution and 95 % overall completeness. Now the Rs are at 18% and 23%, respectively. But the program failed to refine B factors for several ligands, atoms had high B factors while showing positive Fo-Fc map around them. Occupancy was set to 1 and I also tried to reset B to mean B of the whole PDB. Any of you seeing this phenomenon? Thanks! Shown below is HEPES that has high B factor and positive density around it after refinement: [cid:[email protected]] Best regards, Tongqing Tongqing Zhou, Ph.D. Co-head and Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 761-7068 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

4 8

phenix fails to configure on fedora 20
by abhisek Mondal 04 Nov '16

04 Nov '16

Hi, I'm using Fedora 20 on a 4 core laptop. When I tried to install phenix it gave following error. Same version installed fine in my workstation but keep failing here. Please help me out here. Thanks. *[root@viralhost phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6]# ./install * * ==========================================================================* * Phenix Installation* * version: 1.10.1-2155* * machine type: intel-linux-2.6* * OS version: 3.19.8-100.fc20.i686* * destination: /usr/local/phenix-1.10.1-2155* * # of processors: 4* * =========================================================================* *Configuring Phenix components...* *Traceback (most recent call last):* * File "./bin/install.py", line 262, in <module>* * installer(sys.argv[1:]).install()* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 185, in install* * self.install_from_binary()* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary* * self.reconfigure(log=log)* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure* * call(args=args, log=log, verbose=self.options.verbose)* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/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-1.10.1-2155/base/bin/python /usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 126* -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*

4 5

Phenix version 1.11.1 released
by Paul Adams 03 Nov '16

03 Nov '16

The Phenix developers are pleased to announce that version 1.11.1 of Phenix is now available (build 1.11.1-2575). 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 omit maps without bulk solvent in omitted region, automated sharpening of cryo-EM and crystallographic maps, and segmentation of maps. Improved NCS search. New automated model-building tools for low-resolution maps - especially cryo-EM, tools for matching chains (both residues and direction), multiple improvements to phenix.real_space_refine and addition of new GUI. Improved model geometry restraints, many improvements to Phaser, improved validation incorporating new MolProbity features, simplified Rosetta installation, improved support for Amber, updated dependencies, Unicode support in GUI, new unified interface for atom selections. - General - Improved geometry restraints: - Conformation-Dependent Library for omega added (omega_cdl=True) - Installation - Rosetta installation centralised for phenix.rosetta_refine, phenix.mr_rosetta and ERRASER - Improved NCS search procedure with simplified parameters. Provides status of user-supplied NCS groups during validation (refused/modified/ok) - Updated dependencies - biopython 1.64 -> 1.66 - sphinx 1.2.2 -> 1.4.4 - ipython 2.1.0 -> 3.2.1 - pip 6.0.7 -> 8.0.2 - Neutron scattering tables: support ions - Amber refinement - Alpha release dev-2203 - GUI - New interfaces - phenix.map_comparison - phenix.polder - phenix.structure_search - phenix.real_space_refine - New selection editor - Unified interface for selecting atoms - Secondary structure annotations - NCS groups - TLS groups - Refinement strategy options - Unicode support - Non-ASCII characters are supported for most fields (e.g. file paths and job titles) - Using non-ASCII characters in projects/jobs will prevent earlier versions that do not have Unicode support from opening the project list correctly - Migrated validation after phenix.refine to use regular MolProbity for consistency (older versions of Phenix will not open new jobs) - phenix.real_space_correlation can now accept map files - phenix.molprobity can now accept map files - Updated dependencies for Linux - libpng 1.2.52 -> 1.5.26 - freetype 2.4.2 -> 2.6.3 - gettext 0.18.2 -> 0.19.7 - glib 2.12.11 -> 2.46.2 - expat 1.95.8 -> 2.1.0 - fontconfig 2.3.95 -> 2.11.1 - render 0.8 -> 0.11.1 - xrender 0.8.3 -> 0.9.7 - xft 2.1.2 -> 2.3.2 - pixman 0.19.2 -> 0.34.0 - cairo 1.8.10 -> 1.14.4 - pango 1.16.1 -> 1.38.1 - atk 1.9.1 -> 2.18.0 - libtiff 3.6.1 -> 4.0.6 - gtk+ 2.10.11 -> 2.24.29 - matplotlib 1.3.1 -> 1.5.1 - Maps - phenix.polder calculates omit maps which exclude the bulk solvent around the omitted region. This way, weak densities possibly obscured by bulk solvent may become visible. - phenix.model_map: Given PDB file calculate model map and output as CCP4 formatted binary map file. - phenix.mask: Given PDB file calculate bulk-solvent mask and output as CCP4 formatted binary map file. - phenix.auto_sharpen: Optimizes resolution dependence of a map to improve clarity - phenix.segment_and_split_map: Carries out segmentation of a map - Model-building - phenix.map_to_model builds models in low-resolution maps - builds any combination of RNA/DNA/protein - if NCS present, builds the asymmetric unit of NCS and expands to the entire map - phenix.segment_and_split_map breaks up a map into the asymmetric unit of NCS and further subdivides that into contiguous regions of density - phenix.chain_comparison compares CA or P atoms of two models and identifies how many residues match and how many are in the same direction - phenix.real_space_refine: - Support output of refined model in mmCIF format - ADP refinement runs by default at the last macro-cycle. Several CPUs can be used to speed up refinement: use nproc=NUMBER_OF_CPUs parameter for this. - phenix.model_idealization: tool to idealize model geometry while staying as close as possible to the starting model. Currently proteins only. Idealize covalent geometry and secondary structure, as well as eliminate rotamer and Ramachandran plot outliers, C-beta deviations. - phenix.geometry_minimization - ability to use reference torsion restraints - ability to use NCS constraints - phenix.phaser - SOLUTION HISTORY tracks solution through positions in RF/TF/PAK/RNP peak lists - selection by CHAIN and MODEL for PDB coordinate entry - automatic search number for single search ensemble - packing 'trace' molecule can be entered independently of coordinates and map - read TNCS/anisotropy binary files to avoid refinement, when running through scripts - write tNCS and anisotropy parameters to binary files (non-python interface) - default reading of I (or failing that, F) from mtz file (LABIN optional) - trace for ensembles from maps = hexgrid of 1000+/-100 points - trace for ensembles from coordinates above 1000 Calpha = hexgrid of 1000+/-100 points - trace for ensembles from coordinates twixt 1000 atoms and 1000 Calpha = Calpha atoms - trace for ensembles from coordinates under 1000 atoms = all atoms - packing by pairwise percent only, other packing modes obsoleted - packing test during FTF run by default with 50% pairwise packing cutoff - automatic tNCS NMOL determination in presence of commensurate modulation - added MODE GIMBLE, which splits ensembles by chain for rigid body refinement - support for unicode - solution coordinates placed nearest to input coordinates if possible - phenix.reduce - Updated reduce_wwPDB_het_dict as of Aug 12, 2016 - New script for updating het dict - Reduce no longer rotates methionine methyls by default. -DOROTMET flag reinstates old behavior - phenix.ramalyze - Improved handling of residue connectivity - Summary statistics provided for altloc A specifically where multiple altlocs present 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 ] --

1 0

phenix gui starting up for one, not for other users
by wtempel 02 Nov '16

02 Nov '16

Hello, we run phenix on a ubuntu 14.04 (x86_64) box. Phenix is installed in user x’s home directory. After running . ~x/prog/phenix-1.11.1-2575/phenix_env.sh; phenix, and some *setlocale* warnings, the phenix GUI will show up on the screen for user x. User y, after . ~x/prog/phenix-1.11.1-2575/phenix_env.sh; phenix, will get *setlocale* warnings, a white credit screen (briefly), but the GUI will not show up, but *phenix* does not exit. User does get the expected error messages after typing phenix.molprobity_1.11.1-2575 without specifying input coordinates, as does user y get the (older) GUI upon . ~x/prog/phenix-1.10.1-2155/phenix_env.sh; phenix. Do you have any suggestions as to how I can enable user y to use the 1.11.1 GUI? Thank you. Wolfram Tempel

2 4

postdoc jobs at Oxford
by Cell Guidance 02 Nov '16

02 Nov '16

Hello, May I please draw your attention to two excellent postdoc opportunities at the University of Oxford. Further information is available via the links below. Application deadlines are 30 November and 1 December 2016. Postdoc in Structural Biology: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Postdoc in Cell Biology: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Many thanks, Elena Dr. Elena Seiradake Dept. of Biochemistry, University of Oxford South Parks Road, Oxford, OX1 3QU, U.K.

1 0

Viewing different residues in the same location in Coot.
by Nigel Moriarty 29 Oct '16

29 Oct '16

Folks Phenix has the ability to refine two different amino acids (using alt. loc.) in the one place like in 1ejg. You can read more about it here. https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12 This crashes Coot until you add allow_duplicate_sequence_numbers() to $HOME/.coot.py in OSX or the appropriate place on Windows. For Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/ directory for configuration - these can be found (added to) the directory in which Coot was installed (e.g. C:\WinCoot). Nigel PS While you're at it, why not add these lines below to automatically load FEM and polder maps. set_auto_read_column_labels("FEM", "PHIFEM", 0) set_auto_read_column_labels("mFo-DFc_polder", "PHImFo-DFc_polder", 1) --- 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

1 0

rosetta.build_phenix_interface errors
by Gerhard Fischer 28 Oct '16

28 Oct '16

I am having some trouble setting up phenix.rosetta_refine on my Kubuntu 16.04 LTS-system. I've been following the instructions found here: https://www.phenix-online.org/documentation/reference/rosetta_install.html The installation/compilation of Rosetta as such (rosetta_src_2016.37.58930_bundle.tgz) worked fine, and so did installing the latest version of Phenix - here, I've tried both the binary available for download (phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6) and a self-compiled version (phenix-installer-1.11-2567-source). But when running rosetta.build_phenix_interface (both with nproc=6 or no multiple processor options set), the compilation crashes at some point. This takes quite a while, and I suspect most parts get compiled, but it does not run to completion. Any ideas? I attach the output of the error message below. Best wishes, Gerhard ------ stdout ---- g++ -o build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/scoring/cryst/PhenixInterface.os -c -std=c++11 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/5.4 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)': src/core/scoring/cryst/PhenixInterface.cc:253:34: error: no matching function for call to 'core::pose::Pose::dump_pdb(char [256], const char [2])' pose_asu.dump_pdb( pdbout , "1" ); ^ In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0: src/core/pose/Pose.hh:1518:2: note: candidate: bool core::pose::Pose::dump_pdb(const string&) const dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1518:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1521:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&) const dump_pdb(std::ostream & out) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1525:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long unsigned int>&) const dump_pdb( ^ src/core/pose/Pose.hh:1525:2: note: no known conversion for argument 1 from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}' src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)': src/core/scoring/cryst/PhenixInterface.cc:916:34: error: no matching function for call to 'core::pose::Pose::dump_pdb(char [256], const char [2])' pose_asu.dump_pdb( buffer , "1" ); ^ In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0: src/core/pose/Pose.hh:1518:2: note: candidate: bool core::pose::Pose::dump_pdb(const string&) const dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1518:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1521:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&) const dump_pdb(std::ostream & out) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1525:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long unsigned int>&) const dump_pdb( ^ src/core/pose/Pose.hh:1525:2: note: no known conversion for argument 1 from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}' src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)': src/core/scoring/cryst/PhenixInterface.cc:244:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:375:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)': src/core/scoring/cryst/PhenixInterface.cc:914:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1080:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'std::__cxx11::string core::scoring::cryst::PhenixInterface::calculateDensityMap(core::pose::Pose&, bool)': src/core/scoring/cryst/PhenixInterface.cc:1100:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1109:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(".."); ^ scons: *** [build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors. --------- stdout end ------ -- Gerhard Fischer, PhD Postdoctoral Research Associate University of Cambridge Department of Biochemistry 80 Tennis Court Road CB2 1GA Cambridge United Kingdom --- This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

2 1

Fix coordinates of one single residue
by ancacarl 28 Oct '16

28 Oct '16

Hi, I'm working on the refinement of a protein mutated with an unnatural amino acid that is present as two rotamers. Whenever I do refinements, one of the rotamers moves away from the electron density map. I therefore would like to fix the coordinates for this amino acid only while continuing the refinement of the rest of the protein. Is there a way in Phenix to do this? Any advice is welcome. Best regards, Anna-Carin

4 3

Fwd: Re: AW: phenix.real_space_refine
by Pavel Afonine 28 Oct '16

28 Oct '16

Hi Julia, > but I need to try different weightings to find the optimal one, so > this is not an option. no need to try different weights - the program does this for you automatically. If it doesn't - please report a bug. All the best, Pavel

1 0

GUP deadline approaching for APS Beamtime at NE-CAT
by Salbego, Cyndi 27 Oct '16

27 Oct '16

NE-CAT is accepting GUP proposals for the 2017-1 run cycle. Please choose 24-ID-C or 24-ID-E as your first choice to be scheduled with NE-CAT! The 24-ID-C beamline can deliver X-rays in the range of 6 to 21 keV or ~2.1 to 0.5 Å. This covers most of the popular elemental edges for phasing. This wide energy-range also makes the beamline well suited for ultra high-resolution data collection and soft X-ray sulfur SAD phasing. The beamline is equipped with an optional kappa goniometer for optimal alignment of crystals. A Pixel Array Detector (PAD), Pilatus-6MF, installed on the 24-ID-C beamline helps measure very weak Bragg reflection intensities due to its noise-less readout technology and also provides a very fast data collection capability in shutter-less data collection mode. The 24-ID-E beamline is a fixed energy microdiffraction beamline delivering X-rays at 12.66 keV, optimized for Se-SAD experiments. It is equipped with a CCD-based ADSC Quantum 315 detector. Both beamlines are equipped with state-of-the-art instrumentation to handle advanced data collection methods. MD2 microdiffractometers installed at both beamlines provide very clean beams from 5 microns to 100 microns in diameter and have exceptional sample visualization systems capable of visualizing micron-sized crystals with extreme clarity. Deadline Friday, October 28, 2016 for: - New General User Proposals (GUPs) - New Beam Time Requests for APS run 2017-1 (1/31/2017 - 4/24/2017) on existing active proposals - Partner user proposals (PUPs) - CAT Member Proposals - APS Beamline Staff Proposals - CAT Beamline Staff Proposals The GUP system (https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page) will accept proposals and beam time requests until 11:59 pm (Chicago time) on October 28, 2016. However, User Office support will not be available after 5:00 pm that day. If you feel you may need help during the submission process, please create your proposal as early as possible. For questions about the GUP system or the proposal submission process, please contact gu_program(a)aps.anl.gov<mailto:[email protected]>. For guidance on the Proposal System, see https://www1.aps.anl.gov/Users-Information/About-Proposals/Concepts-Definit…. For general inquiries, please feel free to contact the User Office (630-252-9090, apsuser(a)aps.anl.gov<mailto:[email protected]>) Cyndi Salbego Administrator, NE-CAT 630.252.0689

1 0

tNCS
by Huyton, Trevor 25 Oct '16

25 Oct '16

Dear All, I have been struggling for while with a Molecular replacement problem for a large complex(3 proteins) with 2 copies per ASU. I have a small but 100% model for one of the components but this contributes only 12% of ASU (2 molecules) a much poorer <20% model that contributes the majority 80% of the ASU Space group is P222>P212121 best MR is in P21221. I have strong tNCS as seen in native patterson and phaser chooses this top peak in MR runs: There was 1 non-origin distinct peak (i.e. over 20% of origin peak and more than 15 angstroms from the origin) Sorted by Height ---------------- Height Distance Vector 56.0% 126.4 : FRAC +0.5000 +0.5000 +0.3500 (ORTH 63.0 88.0 65.4) Molrep also uses the same tNCS vector: --- Check Patterson for pseudo-translation --- PST_limit : 0.125 of origin peak INFO: pseudo-translation was detected. Origin Patterson peak: P,P/sig : 26479.002 239.412 1 Patterson peak : p,P/sig : 13591.399 122.888 2 Patterson peak : P,P/sig : 2506.590 22.664 3 Patterson peak : P,P/sig : 1517.345 13.719 Peak 1: trans.vector /ort/ : 62.995 88.023 65.691 trans.vector /frac/: 0.500 0.500 0.352 Peak 2: trans.vector /ort/ : 0.000 0.000 55.510 trans.vector /frac/: 0.000 0.000 0.297 Peak 3: trans.vector /ort/ : 58.238 88.023 65.730 trans.vector /frac/: 0.462 0.500 0.352 INFO: translation vector of peak 1 will be used. My question is how does this affect my MR with the smaller component? Is it exactly the same vector as the larger component? Thanks Trevor

1 0

Re: [phenixbb] phenix.real_space_refine
by Pavel Afonine 25 Oct '16

25 Oct '16

On 10/24/16 23:50, Pavel Afonine wrote: > I think "weight=1" may be a troublemaker.. It may be too far from > what's optimal (that program determines by default if you don't > specify any weight) and that may result in clashes that happen during > refinement. Of course, something else may cause this as well. > > Pavel > > On 10/24/16 20:07, Oleg Sobolev wrote: >> Hi Julia, >> >> In addition to Dorothee's response to your another e-mail, I would >> indeed recommend check the model geometry, in particular, bad atomic >> clashes (where 2 atoms are very close to each other). You can find >> them in the .geo file which should be created by this point or in >> log, under "Nonbonded interactions:". The worst clashes will be the >> first in the list. >> >> Best regards, >> Oleg Sobolev. >> >> On Mon, Oct 24, 2016 at 3:19 AM, Flis, Julia <julia.flis(a)charite.de >> <mailto:[email protected]>> wrote: >> >> Hello, >> >> my question is about the Phenix real space refinement. I am using >> the Phenix version phenix-1.11-2563. >> >> My command looks as follows: >> phenix.real_space_refine secondary_structure.enable=true >> Model.pdb VOL.map elbow.Model_pdb.001.cif Model.pdb_ss.eff >> resolution=3.8 weight=1 >> >> My problem is that the refinement suddenly stops during the first >> refinement cycle: >> >> >> >> Model_real_space_refined.log says: >> >> ********************** REFINEMENT MACRO_CYCLE 1 OF 5 >> ************************* >> ------------------------------------------------------------------------------- >> Update NCS operators >> ******************** >> ------------------------------------------------------------------------------- >> Update rotamer restraints >> ************************* >> ------------------------------------------------------------------------------- >> Global refinement >> ***************** >> END >> >> >> In the shell I get this : >> >> [...] >> distance: 184426 - 184921: 3.388 >> distance: 184428 - 184920: 3.342 >> distance: 184448 - 184898: 3.373 >> distance: 184449 - 184897: 3.187 >> distance: 184491 - 184860: 3.066 >> distance: 184531 - 184770: 3.203 >> distance: 184554 - 184746: 3.137 >> >> then it stops and the only files generated are >> Model_real_space_refined.log and Model_initial.geo. >> >> Could you give me an advise? I have no clue what the problem >> could be. >> >> Thank you, >> >> Julia >> >> >

1 0

Post for Ass. Prof. position
by Nigel Moriarty 25 Oct '16

25 Oct '16

Dear Phenix community, An *Assistant Professor position in microbiology or biochemistry* (Position # 22809) is currently open in the Department of Microbiology, University of Manitoba, Canada. Structural biology (protein X-ray crystallography) is a key strength of our Department and so applicants with such a background are encouraged to apply. Please see the ad below for details. *For further information contact the Search Committee Chair <Deborah.Court(a)umanitoba.ca <Deborah.Court(a)umanitoba.ca>>. The closing date for receipt of applications is Friday, January 6, 2017* ——— The Department of Microbiology invites applications for a full-time tenure-track position at the Assistant Professor level, commencing July 1, 2017, or on a date hing and research. Outstanding candidates in any area of Microbiology or Biochemistry will be considered, with particular emphasis on candidates who will complement or extend the department’s strengths. The successful candidate will have a Ph.D. and preferably post-doctoral experience or industry experience or other distinguishing attributes in host-microbe interactions, antibiotic resistance and drug discovery, structural biology, protein and membrane biochemistry, systems microbiology, and industrial and applied microbiology, or a related field. Duties will involve research, including the establishment of an externally funded research program, undergraduate teaching, graduate teaching and supervision, and service-related activities. The successful candidate will have a track record of high quality scholarly research leading to peer assessed publications; will either have, or demonstrate the potential to establish, an independent, innovative, scholarly, externally fundable research program; will have demonstrated strength in or strong potential for outstanding teaching contributions; and will exhibit evidence of the ability to work in a collaborative environment. Salary will be commensurate with experience and qualifications. To enhance our department and create role models for a diverse population of students, we particularly invite application from those who can support and enhance our diversity, including women, Indigenous peoples, other visible minorities, and those committed to a diverse environment. The Department currently has twelve full time tenured and tenure track faculty members and three Instructors, and offers a full range of both undergraduate and graduate programs in Microbiology and Biochemistry. The Department has a well-established and equipped research facility, including X-ray crystallography and large scale mammalian and prokaryotic cell culture facilities, as well as access to state of the art light microscopy, electron microscopy, and small angle x‑ray scattering instrumentation, and is supported by strong research links with other University of Manitoba departments including Chemistry, Biological Sciences, Physics, Biosystems Engineering, Biochemistry and Medical Genetics, and Plant Science and with the National Microbiology Laboratory of the Public Health Agency of Canada in Winnipeg. Further information about the Department can be obtained from <www.sci.umanitoba.ca/microbiology>. Winnipeg is the largest city in the Province of Manitoba. The city has a rich cultural environment, including symphony, opera, dance, theatre, and ethnic festivals and professional hockey and football. The region provides ample opportunities for outdoor recreation in all seasons. Learn more about Winnipeg at <winnipeg.ca>. The University of Manitoba is strongly committed to equity and diversity within its community and especially welcomes applications from women, members of racialized communities, Indigenous persons, persons with disabilities, persons of all sexual orientations and genders, and others who may contribute to the further diversification of ideas. All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority. *Applications including a curriculum vitae, a description of teaching philosophy, a summary of research interests, a three page research plan and contact information for three references should be sent to <Deborah.Court(a)umanitoba.ca <Deborah.Court(a)umanitoba.ca>> (a single PDF file is preferred). Please ensure to specify position number 22809 in the application. For further information contact the Search Committee Chair at <Deborah.Court(a)umanitoba.ca <Deborah.Court(a)umanitoba.ca>>. The closing date for receipt of applications is Friday, January 6, 2017.* Application materials, including letters of reference, will be handled in accordance with the Freedom of Information and Protection of Privacy Act. Please note that curricula vitae may be provided to participating members of the search process. -------- Brian ============================== Brian Mark, MSc, PhD Associate Professor Department of Microbiology & Department of Biochemistry and Medical Genetics Mailing/Courier address: Department of Microbiology Rm 213 Buller Building University of Manitoba 45 Chancellor's Circle Winnipeg, Manitoba CANADA R3T 2N2 Phone (204) 480-1430 Fax (204) 474-7603 Web: http://home.cc.umanitoba.ca/~bmark/Welcome.html 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

1 0

Re: [phenixbb] XN-refinement
by Pavel Afonine 17 Oct '16

17 Oct '16

>> this is good to hear, and this demonstrates the power of using more data. The only issue here, as I mentioned before, is that in joint XN refinement we refine one single model against two data sets, while ideally it should be two models in order to account for genuine unique information that is contained in X-ray and neutron data. This will be addressed at some point. >> > Out of curiosity, could you elaborate on why it would be preferred to refine two separate models? It seems to me, admittedly not having any experience with neutron diffraction, that the ultimate goal is to model the system of the crystal, and given 2 data sets, we would want to create the single model describing the structure in the crystal that best agrees with all the available data. Are the neutron and X-ray data so different that using them for joint refinement is disadvantageous? I think I wrote that already in previous email.. Structures corresponding to two data sets are of course overall similar may be different in local details: - Different X-H(D) distances (see figure 4 here: http://journals.iucr.org/d/issues/2010/11/00/dz5209/index.html) - Different data collection temperatures: -- Different B factors; -- Different visible water structure; -- Different local disorder (that may be captured as distinct conformations at low temperature, but may be blurred at higher temperature); - Different completeness and resolution of one data set may allow features in one model corresponding to this data set that may not be supported by the other data set. For example, you may see a well resolved water with one or two D in neutron map but you may not even see any water at all in X-ray map, or the other way around. - etc etc etc. So it is advantageous to use both X-ray and neutron data sets together but these nuances need to be carefully taken care of which isn't the case in current implementations of joint XN refinement protocols. This makes a good room for future improvements. Pavel

3 2

constrain insertion codes to unit occupancy?
by van den Bedem, Henry 16 Oct '16

16 Oct '16

Hi: I’m refining a site where there’s two compounds, each at partial occupancy. I modeled that using alt codes and insertion codes combined, like this ATOM 6500 CA ACYS B 101B ATOM 6490 CA BXXX B 101A How can I constrain the occupancies so that they sum to unity? I tried several option, but the distinct insertions seem to refine independently. Sorry if a similar question has been posted before, but I could not find a solution searching phenixbb. Thanks! Henry

4 4

XN-refinement
by Johannes Schiebel 15 Oct '16

15 Oct '16

Hi everyone, I am currently working on an X-ray/neutron (XN) joint refinement using phenix.refine. As it should be, H/D coordinates and ADPs at exchangable sites are refined to equal values when using Phenix version 1.10.1-2155 and neutron data only. This is also stated in the paper describing the development of the method (Afonine et al. (2010) Joint X-ray and neutron refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 66, 1153-1163) as the default behavior: "Currently, phenix.refine maintains the H and D atoms at coinciding positions and constrains their ADPs to be equal to each other". However, when switching to XN-refinement using the same Phenix version, H and D atoms refine to different coordinates and ADPs, which should not be the case as it leads to unrealistic artifacts as can be seen from the deposited PDB 3X2P: ATOM 186 H AALA A 13 3.486 -18.200 -14.123 0.38 14.54 H ATOM 187 D BALA A 13 3.488 -18.195 -14.111 0.62 38.07 D In this example, the D-occupancy is likely overestimated, while the H-occupancy is underestimated because the ADPs refine to very different values, which is chemically not reasonable. Hence my question: How can I treat my data in a way that ADPs and coordinates refine to the same values at exchangeable H/D sites also for XN-refinement? Is there a specific keyword I am currently overlooking or do I have to use another Phenix version? I would be really glad to receive your feedback. Thanks in advance! Kind regards, Johannes

4 9

Unknown parameter file format
by Jan van Agthoven 12 Oct '16

12 Oct '16

Hi everyone, I used my refinement parameters in the following format in the latest phenix: custom_par.params And it returned: Sorry: Unknown file format: custom_par.params Anyone knows how to solve this? Thanks, Jan

2 1

Re: [phenixbb] Highly anisotropic data
by Pavel Afonine 07 Oct '16

07 Oct '16

Hi Kostya, phenix.resolution reports effective resolution of data set. It is based on methods described here: J. Appl. Cryst. (2015). 48, 589-597 Acta Cryst. (2013). D69, 1921-1934 As I pointed out before, a single number for highest resolution isn't very informative unless you show data completeness per resolution (in phenix.refine log file it is reported in the beginning of macro-cycles right after bulk-solvent step). Pavel On 10/7/16 00:15, Kogan, Konstantin wrote: > Dear all, > > Thank you for your comments. The maps are not that bad, and actually > from biological point of view we do see everything we want. One of the > questions is how to report the parameters for the structure, as I have > a feeling that the effective resolution is much lower than 2.64Å, > which is the current limit, and the mean B value is twice higher than > estimated Wilson B value. All together it seems that this is the data > I have, but I would like to be sure, that I have got maximum out of it. > > I attach the xtriage log file for more information, if needed. Also I > attached the example of a good map region at 1.6 sigma and a bad map > region at 1.0 sigma. > > I have also tested to refine at 2.8, 2.9, and 3.0, and I haven't seen > much difference in maps quality, but the Rwork/Rfree went down a bit. > > Isn't is seems a bit suspicious 2.64Å resolution, > Rwork/Rfree=0.28/0.31, and mean B value 114? Is there a way to > present/report effective resolution? > > Kostya > > > > > Hi Kostya, > > how complete the data set is? Missing reflections in some resolution > zones between 2.64A and inf may be sufficient to make the effective > resolution lower or much lower than 2.64A which would explain why the > map does not look like what you expect. > > Pavel > > > On 05/10/16 22:53, Randy Read wrote: >> Hi, >> >> As Christian said, the level of anisotropy is not that bad for this >> structure. In terms of what Phenix can do to handle it, first, when >> you solved it by MR, Phaser would have accounted explicitly for the >> anisotropy. In fact, Phaser’s algorithms underlie the anisotropy >> server that produced your plot! Phenix.refine will also refine the >> overall anisotropy parameters. >> >> When you have really severe anisotropy, the current algorithms may >> not account well enough for the differing accuracy of reflections in >> the weak directions. So it can sometimes be helpful to do >> anisotropic pruning of the data in the way that the anisotropy server >> implements it. But this is something to do with some caution, and I >> think you should only press on with it if the maps allow you to see >> things you couldn’t see clearly before. >> >> Best wishes, >> >> Randy Read >> >> ----- >> Randy J. Read >> Department of Haematology, University of Cambridge >> Cambridge Institute for Medical Research Tel: +44 1223 336500 >> Wellcome Trust/MRC Building Fax: +44 1223 336827 >> Hills Road E-mail: rjr27(a)cam.ac.uk >> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk >> >>> On 5 Oct 2016, at 20:32, Christian Roth <christianroth034(a)gmail.com> >>> wrote: >>> >>> Hi Kostya, >>> >>> I have seen worse data than that, which are ususally treated quite >>> well within phenix using standard parameters. With a resolution of >>> about 2.7 Ang. I wouldn't expect to see waters and also just well >>> ordered side chains, whereas more flexible ones just give some >>> "bumps" pointing away from the main chain density. Though without a >>> picture or something else it is difficult to say if your maps are >>> really unusually bad. >>> >>> Cheers >>> >>> Christian >>> >>> Am 05.10.2016 um 07:47 schrieb Kogan, Konstantin: >>>> Dear all, >>>> >>>> I have highly anisotropic data. I was able to solve the structure >>>> by MR, and refine it with phenix.refine to Rwork/Rfree=0.28/0.31 >>>> with Resolution cutoff 2.64Å and mean B values 114, which is pretty >>>> high for such resolution. Though the overall structure makes sense, >>>> the maps are quite featureless, no water molecules, and side-chains >>>> refinement is a problem. I have tested how the data is anisotropic >>>> with Diffraction Anisotropy Server (see attached image), which >>>> shows clearly, that we don't really have data to 2.64Å in all >>>> directions. Though, there are other servers/programs that can deal >>>> specifically with anisotropic data e.g. STARANISO anisotropy server >>>> and then refine with BUSTER, I would like to know if it's possible >>>> still to use Phenix with some more advance parameters to actually >>>> address the issue of anisotropy and to get maximum out of the data. >>>> The space group is P61 2 2, cell parameters are 73, 73, 453, 90, >>>> 90, 120 and I have high multiplicity data, but no NCS. >>>> >>>> Thanks in advance for any input, >>>> >>>> Kostya >>>> -- >>>> Konstantin (Kostya) Kogan >>>> Postdoctoral researcher >>>> Pekka Lappalainen's Lab >>>> Institute of Biotechnology >>>> University of Helsinki >>>> Helsinki, Finland >>>> Mobile: +358-(0)45-8994342 >>>> >>>> >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> Unsubscribe: >>>> phenixbb-leave(a)phenix-online.org >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> Unsubscribe: phenixbb-leave(a)phenix-online.org

1 0

Option to select array from mtz in phenix.real_space_refine?
by Oliver Clarke 06 Oct '16

06 Oct '16

Hi, I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled). However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time. Cheers Oli

3 5

Highly anisotropic data
by Kogan, Konstantin 06 Oct '16

06 Oct '16

Dear all, I have highly anisotropic data. I was able to solve the structure by MR, and refine it with phenix.refine to Rwork/Rfree=0.28/0.31 with Resolution cutoff 2.64Å and mean B values 114, which is pretty high for such resolution. Though the overall structure makes sense, the maps are quite featureless, no water molecules, and side-chains refinement is a problem. I have tested how the data is anisotropic with Diffraction Anisotropy Server <https://services.mbi.ucla.edu/anisoscale/> (see attached image), which shows clearly, that we don't really have data to 2.64Å in all directions. Though, there are other servers/programs that can deal specifically with anisotropic data e.g. STARANISO anisotropy server <http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi> and then refine with BUSTER, I would like to know if it's possible still to use Phenix with some more advance parameters to actually address the issue of anisotropy and to get maximum out of the data. The space group is P61 2 2, cell parameters are 73, 73, 453, 90, 90, 120 and I have high multiplicity data, but no NCS. Thanks in advance for any input, Kostya -- Konstantin (Kostya) Kogan Postdoctoral researcher Pekka Lappalainen's Lab Institute of Biotechnology University of Helsinki Helsinki, Finland Mobile: +358-(0)45-8994342

4 3

Planarity restraint ignored when dist_esd equal to 0
by Keitaro Yamashita 28 Sep '16

28 Sep '16

Dear PHENIX developers, My colleague noticed that planarity restraint of a ligand was ignored when a cif file in CCP4 monomer library was given to phenix.refine. The cif file was $CLIBD_MON/3/3PG.cif. This was because phenix (mmtbx) ignores planarity restraint when dist_esd is 0. In the line 2055 of mmtbx/monomer_library/pdb_interpretation.py (phenix-1.10.1), plane_atom is not added to the list when (plane_atom.dist_esd in [None, 0]) is True. _chem_comp_plane_atom.dist_esd in 3PG.cif (ccp4-7.0) is all zero except the first atom in the plane definition. As far as I checked, there is no cif file where dist_esd of the first atom of plane is zero. At least, it would be helpful if phenix shows warning in this case. Best regards, Keitaro

6 9

How to define Fobs labels for phenix.refine in command line mode
by Karthikeyan Subramanian 27 Sep '16

27 Sep '16

Dear All, Is it possible to define the Fobs (or) Iobs labels for phenix.refine in command line mode? Thanks Karthikeyan S. IMTECH, Chandigarh India

2 2

Rotamers of unnatural halogenated amino acids
by ancacarl 27 Sep '16

27 Sep '16

Hi, I'm working on the refinement of a protein mutated with an unnatural amino acid that contains one bromine atom. This particular amino acid is present as two rotamers. I've managed to introduce and do refinements with these two unnatural, brominated rotamers in Phenix, but the problem is that when shooting the protein with X-rays about 30-40% of the bromine atoms get knocked off. This means that the sum of the occupancies for the bromine atoms of the rotamers needs to be less than 1.00. However, the total occupancy of all the other rotamer atom pairs must be 1.00. Is there a way in Phenix to refine rotamers of brominated, unnatural amino acids, and at the same time have the total occupancy less than 1.00 for the Br atoms only? Any advice how to solve this is welcome.

2 1

phenix.real_space_refine - mmcif output?
by Oliver Clarke 27 Sep '16

27 Sep '16

Any chance of getting mmcif output in phenix.real_space_refine? Or does it exist and I have just overlooked the option? Right now I can use mmcif as input, but the refined coordinates are still written as pdb (hybrid32). The PDB unfortunately doesn’t accept hybrid32, so I always need to convert to mmcif with phenix.pdbtools prior to deposition - no big deal but would make life easier for large-ish structures. Cheers Oli.

2 1

Registration open: Future of Fragments symposium - Diamond, 28/29 Nov 2016
by Frank von Delft 23 Sep '16

23 Sep '16

Dear all Registration is now open for the Future of Fragments symposium on 28/29 November at Diamond Light Source, UK. http://www.diamond.ac.uk/Home/Events/2016/Future-of-Fragments-Symposium.html Places will be tight, so register early to give us time to gauge whether we must adapt plans. _Overview_ Crystal-based fragment screening of novel protein targets linked to disease has truly come of age: Diamond's XChem facility has been operating a regular user program since 2015, with other synchrotrons soon to follow suit. A progression of user projects have confirmed the power of this approach to discover both diverse chemotypes and unexpected mechanisms of action, especially allosteric binders. At the same time, the continued success in unearthing a rich array of fragment hits has now decisively shifted the bottleneck onto the question of how to translate hits into high potency leads. This challenge has highlighted the need for efficient and scalable methodologies in the areas of library design, label-free assays, computational compound design and the synthesis of complex lead molecules. This symposium aims to highlight the opportunities that must be explored if routine fragment screening is to turn into routine lead discovery. The event will bring together speakers from diverse disciplines to help define the methodology, focus and goals for fragment screening in the coming years. The four sessions will cover: screening methodology; computational methods; new synthetic methods; and automated chemistry.

1 0

Weighting in phenix.real_space_refine
by Oliver Clarke 13 Sep '16

13 Sep '16

Hi all, How does phenix.real_space_refine deal with restraint weighting? Looking at the output of the program, I get the impression that it splits the model up into different chunks, and alters weights locally based on some model/map correlation metric - is this the case (and are there more specific details available), or how does it work otherwise? Cheers, Oliver.

3 7

rosetta installation
by Sebastiano Pasqualato 13 Sep '16

13 Sep '16

Hi there, I am trying to run Phenix Rosetta Refinement on my laptop, which is running MacOSX 10.11.6 (El Capitan) with XQuartz 2.7.9. I have followed the instructions on this page: https://www.phenix-online.org/documentation/reference/rosetta_refine.html <https://www.phenix-online.org/documentation/reference/rosetta_refine.html> and specifically Once you have both a Phenix installation and a Rosetta source distribution, you can build the hybrid system with this command (located in the Phenix tree): rosetta.build_phenix_interface nproc=X Unfortunately, when I do that, the building does not proceed flawlessly, but instead stops with the message the I report below. Has someone gone through the same and can tell me how to set up Rosetta to be used with Phenix? Thanks in advance for the help, Sebastiano Seba@host028:~> rosetta.build_phenix_interface nproc=8 False scons: Reading SConscript files ... xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Running versioning script ... xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun Done. (0.0 seconds) Number of option files updated: 0 Total 3741 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... clang++ -o build/src/release/macos/15.6/64/x86/clang/python/apps/public/AbinitioRelax.o -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/apps/public/AbinitioRelax.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/devel/init.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/devel/init.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/devel/svn_version.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/devel/svn_version.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/init/init.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/init/init.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/DownstreamRMSEvaluator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/DownstreamRMSEvaluator.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/LimitHitsPerRotamerFilter.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/LimitHitsPerRotamerFilter.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchConsolidator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/MatchConsolidator.cc xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun scons: *** [build/src/release/macos/15.6/64/x86/clang/python/apps/public/AbinitioRelax.o] Error 1 clang++ -o build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchEvaluator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/MatchEvaluator.cc <http://matchevaluator.cc/> scons: *** [build/src/release/macos/15.6/64/x86/clang/python/devel/init.os] Error 1 scons: *** [build/src/release/macos/15.6/64/x86/clang/python/devel/svn_version.os] Error 1 scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/init/init.os] Error 1 scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/DownstreamRMSEvaluator.os] Error 1 scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/LimitHitsPerRotamerFilter.os] Error 1 scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchConsolidator.os] Error 1 xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun scons: *** [build/src/release/macos/15.6/64/x86/clang/python/protocols/match/output/MatchEvaluator.os] Error 1 scons: building terminated because of errors. Seba@host028:~> -- 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

2 3

To count crystal contacts along a, b or c?
by vincent Chaptal 08 Sep '16

08 Sep '16

Dear community, I would like to count crystal contacts bewteen ASU and symmetrics along the cell axis (a, b, c). Could someone point to me a way to do this? Thank you very much in advance. vincent -- 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

1 0

Phenix validate without map/mtz?
by Oliver Clarke 08 Sep '16

08 Sep '16

Hi, Would it be possible to allow for running phenix validate without a map/mtz? I dont always want the RSCC information, and it would be useful to be able to get the geometry stats and sequence check without loading a map (which in the case of EM maps can be very large and will presumably slow things down a lot). Cheers, Oliver.

3 3

Data processing
by Sharan Karade 07 Sep '16

07 Sep '16

Dear All, i had collected the data set on the Bruker X-ray machine (home source), it has its in built data processing software, but i want to process it on HKL2000, but the file format is .srfm and it is not read by HKL2000 soft. in our lab we have. So, i tried to change the detector type, then i came to know that we don't have license to bruker detector, So anyone know how to convert these file into .mccd or.mar, so i can process them. Thank you -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

2 1

Post-doctoral position in membrane protein structure and function, University of Oxford, UK
by Maike Bublitz 06 Sep '16

06 Sep '16

Dear all, 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 microbial 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 14th September 2016. PLEASE NOTE: THIS IS A READVERTISEMENT, PREVIOUS APPLICANTS NEED NOT APPLY. Best regards, Maike ************************************************* Dr. Maike Bublitz Associate Professor of Microbial Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom phone: +44 (0)1865 613221 maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk> ************************************************* Dr. Maike Bublitz Associate Professor of Microbial Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom phone: +44 (0)1865 613221 maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk>

1 0

Computational Crystallography Newsletter, Volume 7, Number 2
by Nigel Moriarty 31 Aug '16

31 Aug '16

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. July 2016 <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf> Articles - Working with EIGER data <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=11> - Processing XFEL data with cctbx.xfel and DIALS <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=18> Short Communications - Using Molecular Dynamics Simulations to Enrich the Water Structure in Biomolecular Crystals <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=7> Fitting tips #12 – Twist Tells: better β strands at >3.5Å in x-ray or cryoEM <http://www.phenix-online.org/newsletter/CCN_2016_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

1 0

polder map
by Kaziaa 29 Aug '16

29 Aug '16

Dear Phenix users, i am wondering if anyone has used phenix polder in Windows machine. Any kind of help would me appreciated !! Regards Kazi

3 2

Meaning of "resolution" keyword for phenix.real_space_refine with mrc/ccp4 map input?
by Oliver Clarke 28 Aug '16

28 Aug '16

Hi, What exactly does phenix.real_space_refine do with the mandatory "resolution=" keyword when refining a model against a ccp4/mrc formatted map? Is this purely for adjusting restraints etc, or does phenix internally low-pass filter or resample the map based on this parameter? This seems like a basic question, so I apologize if the answer is staring me in the face, but I couldn't see it in the online documentation or in the output of phenix.real_space_refine --help. Cheers Oliver.

6 11

discrepancies between completeness stats
by Kendall Nettles 23 Aug '16

23 Aug '16

Dear PHENIX developers, We are getting a group of structures ready for publication and noticed that the table 1 description of the completeness is showing higher completeness in the last shell than overall. See Table 1, attached, for one example, with completeness at 81.73 (96.75). This table was calculated from the last major release of PHENIX, and was the same on the latest nightly build. The data was highly anisotropic so we truncated it with the UCLA diffraction anisotropy server. Validation program suggests completeness is 13% in highest res shell, which makes more sense with anisotropic data. I also noticed that the refinement log lists the overall completeness at 85% while the validation and table 1 programs give 82%. Thanks for you advice! Kendall

1 0

Merged data for "Table 1"
by Yufan Wu 11 Aug '16

11 Aug '16

Dear all, I am going to generate “Table 1” by Phenix. However, my data.mtz file was merged from 2 HKL file (2 different datasets). What should I input in “unmerged data"? Thank you in advance! Best, Yufan Regards, Yufan Wu The Plueckthun Lab www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>Phone: +41 44 635 5574

2 1

Mg is driving me crazy
by Almudena Ponce Salvatierra 09 Aug '16

09 Aug '16

Dear all, I am refining a structure that showed two positive peaks larger than 8 sigma. I assigned them as Mg ions, since I have them in the crystallization condition and also because it make sense, according to where they are located. However when I refine there's still all this green blob around the already properly placed Mg ions. I don't know why, they don't show large thermal factors or anything suspicious... I'm refining individual sites, individual adps, and TLS groups. The resolution I am talking about is 2.5 A. Any thoughts on this? Thank you very much Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

3 2

Phenix.refine peptide chain break
by Booe, Jason M (HSC) 30 Jul '16

30 Jul '16

Dear all, I am refining a structure after renumbering my chain such that there is a gap in numbering (i.e. chain A ends at 350 and then starts again at 1000) as this has numbering has been recommended for us to use by the PDB for our fusion proteins. I'm having issues with Phenix.refine not understanding that their is still a peptide bond and breaks the chain and pushes the atoms away. There is no TER card between the chains and I've used LINK records as well to no avail. I'm wondering how to properly deal with this. Thanks, Jason

4 5

Refine pixel size of map (for EM data)?
by Oliver Clarke 26 Jul '16

26 Jul '16

Hello, I wonder whether it would be possible to add an option for phenix.real_space_refine to allow refinement of the pixel size of the map (or the unit cell dimensions - just an overall size scale factor), and write out the altered map at the end of refinement. Although we try to calibrate this as best as we are able at the time of data collection, it is never perfect - for example, in one case I have dealt with, our nominal pixel size out of the scope is 1.19 Å, but the pixel size calibrated based on a crystal structure of a fragment of the protein is 1.25 Å. This is not a huge difference, but it is sufficient I think to have a substantial impact on refinement, particularly as regards clash assessment and H-bond/sec struc restraints. In cases where one does not have a solved crystal structure to use for calibration, perhaps refining the pixel size in conjunction with the geometry might be of some use? Cheers, Oli

5 10

Phenix download issues
by Billy Poon 26 Jul '16

26 Jul '16

Dear all, There is currently an issue with our file server, so Phenix downloads are not unavailable. I will update the list when the website is fully functional. -- 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

1 1

Fall 2016 MicroED workshop at Janelia Research Campus (Reminder)
by Hattne, Johan 22 Jul '16

22 Jul '16

Reminder: the deadline for applications for the Fall 2016 MicroED Workshop is August 1, 2016 (11:59 PM EDT). The original announcement is included below. The second installment of the MicroED workshop will be held at Janelia Research Campus (Ashburn, VA) November 13-16, 2016, hosted by Tamir Gonen. MicroED is a cryo-EM method that uses electron diffraction to facilitate structure determination from sub-micron sized 3D crystals of biological material. MicroED uses equipment and procedures that are standard on many cryo-EM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To encourage the widespread use of MicroED we are offering this workshop to teach microscopists how to perform the technique and adopt it at their own institutions. The first MicroED workshop was held in February of 2016 and was heavily oversubscribed. For this reason we are offering a second workshop. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Space in the course is limited. The application deadline is August 1, 2016 (11:59 PM EDT). For more details and to apply, visit https://www.janelia.org/you-janelia/conferences/microed-workshop-1. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

1 0

Berkeley Server Downtime (24 hours, 7/22 - 7/23)
by Billy Poon 21 Jul '16

21 Jul '16

Dear all, On Friday, July 22, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available the next day (7/23) by 5:00 pm Pacific at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- 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

1 0

MolProbity C-beta outliers
by Yufan Wu 19 Jul '16

19 Jul '16

Dear all, Anyone knows the definition of “angle” shown in the report of "MolProbity C-beta position outliers” after refinement ? It means the bond angle or dihedral angle? Between which atoms or planers? I am just wondering the definition of it. Thank you in advance! Best, Yufan Wu Regards, Yufan Wu The Plueckthun Lab www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>Phone: +41 44 635 5574

2 1

MolProbity C-beta outliers
by Yufan Wu 15 Jul '16

15 Jul '16

Dear all, Anyone knows the definition of angle in "MolProbity C-beta position outliers”? See the screenshot below. It means the bond angle or dihedral angle? Between which atoms or planers? I am just wondering the definition of it. Thank you in advance! Best, Yufan Wu Regards, Yufan Wu The Plueckthun Lab www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>Phone: +41 44 635 5574

1 0

Amber in phenix
by R. Gasper-Schönenbrücher 13 Jul '16

13 Jul '16

Hi all, I am trying to run amber from phenix with a standard pdb file, no co-factors etc and struggle already at the phenix.AmberPrep script. For unknown reasons, the .prmtop file stays empty (0 bytes). I have tried to figure out from the amber python scripts, where the problem might be, but didn't find anything obvious (the "self.ns_names" variable stays empty) The leap log files states two problems: 1) ......Nonterminal, was not found in name map. (for every single amino acid) 2) FATAL: Atom .R<MET 1>.A<N 1> does not have a type. (for every single atom) which ends up in: "Failed to generate parameters Parameter file was not saved." There is no .map2 file generated. Phenix version: dev-2463 Amber: Ambertools 16 Every help is highly appreciated. Many thanks! Best, Raphael -- Raphael Gasper-Schönenbrücher Universität Bochum AG Proteinkristallographie, Lehrstuhl für Biophysik, NDEF 04/316 Universitätsstraße 150 44801 Bochum Germany Tel: +49 (0)234-32 27086 Fax: +49 (0)234-32 14762

3 2

How to assign Half occupancy to metal ion in protein crystal
by Sharan Karade 08 Jul '16

08 Jul '16

Dear all, I am refining the protein structure and i want add metal ion in the structure, the site is present in between protein chain and its symmetry mate. when i added metal and refined, it was showing the high B factor and symmetry related metal on the same site. i want to assign the occupancy half and refine but in coot i am unable to do. Is there any method to do this. Thanks in Advance -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

2 1

Question about restrain of a nonstandard peptide
by Yufan Wu 06 Jul '16

06 Jul '16

Dear Phenix Developers/Users, I have a question regarding how to generate a correct restrain for a whole nonstandard peptide and how do run refinement correctly. The nonstandard peptide in my structure is pepstatin A (IVA Val Val STA Ala STA). I manually put the pepstatin A in the density and generated the cif files for IVA and STA and run the refinement with them. After refinement, the whole pepstatin A explored as pieces, which I guess the program treated the pepstatin A as single amino acids. By the way, I also manual input the “LINK” information in the input pdb file as below, LINK C VAL L 3 N STA L 4 1555 1555 LINK N ALA L 5 C STA L 4 1555 1555 LINK C ALA L 5 N STA L 6 1555 1555 And also, when I use the “Real Space Refine Zone” by clicking two atoms for the whole pepstatin A in coot, it exploded again, although I input the same cif file in coot as well. The data quality is not good (2.9 A with CC1/2=12), thus it is difficult to place amino acid individually to fit the destiny. In the PDB, there are several structures containing the pepstatin A, such as 4TVG, 4AUC. They have the pepatatin A sequence as VVVXAX, but none of them lists the constrains. Would you please help me and let me know how can I continue with refinement? Please let me know if you need more information. Thank you vey much! Yufan Wu Regards, Yufan Wu The Plueckthun Lab www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>Phone: +41 44 635 5574

2 1

Glycan refinement in Phenix.real_space_refine
by Simonas Masiulis 06 Jul '16

06 Jul '16

Hi, I want to refine N-linked glycans into an EM density using Phenix.real_space_refine, but it seems the rings get distorted. Does anybody know how to fix this (e.g., is there a way to provide a .cif file)? Thanks a lot! Simonas

2 1

.cif file created by Jligand for used in phenix.model_vs_data
by luzuok 06 Jul '16

06 Jul '16

Dear all, The protein was covalently linked by my ligand and I used JLigand to generate the link record and the .cif file. This file can be used in Refmac successfully. But the .cif file cannot be recognized by phenix.model_vs_data nor phenix.refine. The program runs with the following message: Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 19 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. Any suggestions how to do this would be greatly appreciated. Another question is, how can I generate a restraints file for COOT to do real space refinement? The .cif file is imported in COOT, but when I do real space refinement, the link bond still takes apart. Best wishes! Lu -- 卢作焜南开大学新生物站A202 Lu Zuokun, Ph.D. Candidate College of Life Science, Nankai University

3 4