February 2019 - phenixbb - phenix-online.org

HFIR/SNS Advanced Neutron Diffraction and Scattering Workshop - HANDS 2019
by Meilleur, Flora 22 Apr '19

22 Apr '19

First announcement HANDS 2019 HFIR/SNS Advanced Neutron Diffraction and Scattering Workshop Oak Ridge, TN. June 19 - June 14, 2018 Oak Ridge National Laboratory, in conjunction with North Carolina State University, and support from the National Science Foundation and the Shull Wollan Center - a Joint Institute for Neutron Scattering, celebrates a decade of neutron scattering education in structural biology at ORNL with the HFIR/SNS Advanced Neutron Diffraction and Scattering workshop (HANDS 2019). Detailed information can be found on the workshop web page: https://conference.sns.gov/hands2019/ Application deadline: April 29, 2019 Fellowships to support travel and accommodation are available. No registration fee. The workshop aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Participants of HANDS 2019 will become familiar with neutron techniques with hands-on experiments in sample preparation, crystallography, small angle scattering, reflectometry and neutron spin echo. The workshop is designed for graduate students, post-doctoral fellows and faculty with limited to no experience with neutron sciences. Flora Meilleur, Ph. D Neutron Scattering Scientist, Neutron Scattering Division Oak Ridge National Laboratory Associate Professor, Molecular and Structural Biochemistry North Carolina State University

1 2

12th CCP4/APS Crystallographic School in the US
by Xu, Qingping 11 Apr '19

11 Apr '19

Dear Colleagues, We are pleased to announce the 12th annual CCP4 crystallographic school “From data collection to structure refinement and beyond” will be held on June 17-24, 2019 at Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2019/index.php. Dates: June 17 through 24, 2019 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 15th, 2019. To apply, visit https://www.ccp4.ac.uk/schools/APS-2019/application.php. Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

1 2

mmCIF for deposition
by Patrick Loll 20 Mar '19

20 Mar '19

Hi all, Following the instructions given here: https://www.phenix-online.org/documentation/overviews/xray-structure-deposi… I’m attempting to use mmtbx.prepare_pdb_deposition to insert sequence information into the mmCIF that contains the model coordinates. Unfortunately, the program fails with an error (shown below). The sequence file is FASTA format, and contains an entry for each of the (4) chains in the AU, i.e. >A MSEQNCE… >B MSEQNCE… etc. Any bright ideas? ============this is what happens (vide infra)==================================== [PJL-iMac:blahblah/PJL_final] loll% mmtbx.prepare_pdb_deposition filename.cif seq_name.fasta Starting mmtbx.prepare_pdb_deposition on Mon Oct 1 11:16:23 2018 by loll =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, filename.cif Found sequence, seq_name.fasta Processing PHIL parameters: ------------------------------------------------------------------------------- No PHIL parameters found Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = “filename.cif" } default_model = “filename.cif" sequence_files = "seq_name.fasta" default_sequence = "seq_name.fasta" } Starting job =============================================================================== Validating inputs Using model: filename.cif Using sequence: seq_name.fasta Creating mmCIF block for sequence Traceback (most recent call last): File "/Applications/phenix-1.14-3260/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 9, in <module> run_program(program_class=prepare_pdb_deposition.Program) File "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/cli_parser.py", line 71, in run_program task.run() File "/Applications/phenix-1.14-3260/modules/cctbx_project/mmtbx/programs/prepare_pdb_deposition.py", line 98, in run alignment_params=self.params.mmtbx.validation.sequence.sequence_alignment) File "/Applications/phenix-1.14-3260/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 1190, in as_cif_block_with_sequence assert len(chain.residue_groups) + chain.n_missing_start + chain.n_missing_end == len(sequence) AssertionError (gouts of smoke, terrified squealing) The ‘No PHIL parameters found’ message is concerning, but the program clearly seems to be finding the input file names. Suggestions welcome. 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

3 4

Rotamer restraints in phenix.real_space_refine
by Ashley Pike 01 Mar '19

01 Mar '19

Hi - Am I right in thinking that rotamer restraints behaves differently in latest official release (1.14-3260) compared to last but one official release (1.13-2998)? Issuing rotamer_restraints=True from command line or GUI used to give 0% rotamer outliers in the molprobity analysis at end of log in 1.13-2998 but now in 1.14 gives non-zero for same input model. It is as if they are not being applied. In the old log file it used to clearly print - **Update rotamer restraints*** after every macrocycle, in the 1.14 logs this is omitted. Many thanks, Ashley

3 4

molprobity in phenix 1.14
by Roberto Marabini 26 Feb '19

26 Feb '19

Hi, In the past (phenix 1.13) I have been able to execute molprobity with the command line: ============== phenix.python /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif map_file_name=/home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/molprobity.mrc d_min=2.200000 pickle=True pdb_interpretation.clash_guard.nonbonded_distance_threshold=None nproc=4 pdb_interpretation.clash_guard.nonbonded_distance_threshold=None ================== Unfortunately, for version 1.14 I get the error: ========================== Traceback (most recent call last): File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 310, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 193, in run map_params=params) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/molprobity/__init__.py", line 216, in __init__ molprobity_map_params=map_params.input.maps) File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/experimental.py", line 198, in __init__ from mmtbx.command_line.map_model_cc import get_fsc ImportError: No module named map_model_cc ============== That is, there is an error in the line "from mmtbx.command_line.map_model_cc import get_fsc" By the way, if I just run the command: ============== phenix.python /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif ================== the program is executed without any problem. What should I do in order to execute molprobity.py with the option map_file_name. best wishes Roberto

2 1

real space refine generates non-compliant PDB files
by Edwin Pozharski 23 Feb '19

23 Feb '19

Not sure whether anyone would care now that we got our marching orders to abandon PDB format and move to mmCIF, but the output of phenix.real_space_refine includes a number of lines that are not legit PDB records, i.e. this section ... REMARK 3 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.049 74053 ANGLE : 0.747 12.299 100513 CHIRALITY : 0.052 0.232 11312 PLANARITY : 0.006 0.069 13125 DIHEDRAL : 11.589 179.958 44947 MIN NONBONDED DISTANCE : 2.276 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 5.04 RAMACHANDRAN PLOT: OUTLIERS : 0.30 % ALLOWED : 8.63 % FAVORED : 91.06 % ROTAMER OUTLIERS : 8.76 % CBETA DEVIATIONS : 0 PEPTIDE PLANE: CIS-PROLINE : 3.7037037037 CIS-GENERAL : 0.0 TWISTED PROLINE : 1.85185185185 TWISTED GENERAL : 0.316455696203 REMARK 3 ... This does result in errors when this output PDB file is used as input to other software that is more stringent with format compliance. Cheers, Ed.

2 1

Junior group leader opportunity in infection research (Braunschweig, Germany)
by Blankenfeldt, Wulf 22 Feb '19

22 Feb '19

Dear colleagues, I'd like to bring your attention to a job opening for a junior research group leader at the Helmholtz Centre for Infection Research in Braunschweig, Germany. The opening is broadly for infection research, and structural biologists should also feel encouraged to apply. The HZI has state-of-the-art facilities for x-ray crystallography and, through our participation in the CSSB on the DESY campus in Hamburg, to cryo-EM. We also have a protein sample production facility and equipment for biochemical/biophysical characterization. More details about the position and application requirements (deadline Feb. 28th!) can be found here: https://www.nature.com/naturecareers/job?id=672825 Best regards, Wulf ________________________________ Helmholtz-Zentrum f?r Infektionsforschung GmbH | Inhoffenstra?e 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig R?diger Eichel, Nieders?chsisches Ministerium f?r Wissenschaft und Kultur Gesch?ftsf?hrung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschr?nkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

1 0

run phenix.refine in command line error
by 张士军 18 Feb '19

18 Feb '19

Dear I cannot run the *.params file when I use command line to run phenix.refine. Does have any default *.params file format, which I can edit it according to my case? Can you sent me one if does exist? Thanks . Best regards Shijun

1 0

error installation dev-1.14.3405 - 1.14.3409
by Guenter Fritz 14 Feb '19

14 Feb '19

Dear phenix developers, I get errors trying to install latest builds from 1.14.3405, 3406, 3409 64bit centos6 on Scientific Linux machines still running 6.6 (kernel 2.6.32). 1.14.3395 installed without any problem. The downloaded file is OK. 1.14.3409 64bit centos6 installed on Ubuntu 18.04 without any problem. I also tried to install from source but got the same error output (see below). I googeled some error outputs - looks like some python error. Do I have to update finally? Best regards, Guenter Output trying to install from source: [guenter@msm68 phenix-installer-dev-3409-source]$ ./install --prefix=/home/software/PHENIX/1.14.3409/ --nproc=10 Traceback (most recent call last): File "./bin/install.py", line 20, in <module> from libtbx.auto_build import install_distribution File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_distribution.py", line 75, in <module> from libtbx.auto_build import install_base_packages File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module> from .package_defs import * File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/package_defs.py", line 18, in <module> from .bootstrap import Toolbox File "/home/software/PHENIX/1.14.3409/phenix-installer-dev-3409-source/lib/libtbx/auto_build/bootstrap.py", line 14, in <module> import argparse ImportError: No module named argparse Similar from an installer: [guenter@msm68 phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6]$ ./install --prefix=/home/software/PHENIX/1.14.3405/ Traceback (most recent call last): File "./bin/install.py", line 20, in <module> from libtbx.auto_build import install_distribution File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 75, in <module> from libtbx.auto_build import install_base_packages File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_base_packages.py", line 28, in <module> from .package_defs import * File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/package_defs.py", line 18, in <module> from .bootstrap import Toolbox File "/home/software/PHENIX/1.14.3405/phenix-installer-dev-3405-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/bootstrap.py", line 14, in <module> import argparse ImportError: No module named argparse

2 4

CryoEM post-doctoral position
by Hasan, Syed Saif 08 Feb '19

08 Feb '19

A post-doctoral research position is high-resolution single particle cryoEM is available immediately in my laboratory at the Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan) in Rockville MD. The post-doctoral researcher will have a choice of multiple projects in structural biology of membrane protein complexes involved in cancer and viral pathogenesis. The researcher will have independence to guide the direction of their research and to pursue novel ideas should they find an interesting scientific question related to the general focus of my laboratory. IBBR is home to a large community of structural biologists. Our new cryoEM facility houses a 200 keV Thermo Fisher Talos Arctica microscope equipped with a Gatan K3 direct electron detector. A 200keV Thermo Fisher Glacios microscope equipped with a Falcon III direct electron detector will be acquired soon. A 120 keV FEI Tecnai T12 TEM equipped with a CCD camera is available for negative stain imaging. In addition to the latest cryoEM facilities, IBBR offers access to tools in X-ray crystallography, NMR, small angle X-ray scattering, mass-spectrometry and computational biology, and provides opportunities to work closely in collaboration with scientists in industry and in national labs located nearby (i.e., NIH, NIST). Applicants should have experience in sample preparation, data collection and data processing for single particle cryoEM. Applicants who have received their PhD or MD/PhD degree should email me (sshasan(a)som.umaryland.edu) a single PDF file containing a short cover letter (no more than one page), a detailed curriculum vitae, contact information for three references, and up to 3 reprints of representative first authorship publication(s). The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology University of Maryland School of Medicine 108 N. Greene St., Baltimore, MD 21201 Institute for Bioscience and BiotechnologyResearch (IBBR) 9600 Gudelsky Drive, Rockville, MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan

2 1