- phenixbb - phenix-online.org

lattice symmetry and free-set selection?
by Edward A. Berry 22 Feb '18

22 Feb '18

Where can I find description of the free-r selection parameters: refinement.input.xray_data.r_free_flags { lattice_symmetry_max_delta=5 use_lattice_symmetry=True } ?

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Industrial Biostructures America 2018 conference
by Leonard,Paul G 20 Feb '18

20 Feb '18

Dear all, The inaugural Industrial Biostructures America conference will be held on 20-22 May 2018 at the Hilton La Jolla Torrey Pines Hotel in San Diego, California. Conference registration and accommodation information is available at: https://industrialbiostructuresamerica.org/ This conference brings together structural biologists from across the pharmaceutical and biotech industry to showcase their cutting-edge research. Scientific sessions will cover the following topics: * Cryo-EM * X-ray crystallography * Lead discovery using NMR * Protein design * Membrane crystallography The Abstract submission deadline is 23rd March 2018. We look forward to seeing you there, Paul Leonard Institute Research Scientist MD Anderson Cancer Center pleonard1(a)mdanderson.org<mailto:[email protected]> The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Salbego, Cyndi 18 Feb '18

18 Feb '18

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. We currently have a number of days open in March. Below is a brief description of our beam lines, and links with more information. 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 an Eiger-16M Pixel Array Detector, offering advantages similar to those of the Pilatus-6MF. For more information on our beamlines (beamline and robot manuals): http://necat.chem.cornell.edu To ask about available time please contact Raj Rajashankar (rajashankar(a)anl.gov<mailto:[email protected]>) or Cyndi Salbego (csalbego(a)anl.gov<mailto:[email protected]>) for further information. To apply for General User Time (Rapid Access for current run cycle) please follow this link: https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page Cyndi Salbego Administrator, NECAT 630.252.0689

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9th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 14 Feb '18

14 Feb '18

First announcement 9th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 11 - June 15, 2018 Detailed information: https://conference.sns.gov/biologyneutrons18/ Application deadline: April 30, 2018 The workshop on Neutron Scattering Applications in Structural Biology 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. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Scattering Scientist, Neutron Sciences Directorate Oak Ridge National Laboratory

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Postdoctoral position in membrane protein structure and function at the NIH
by Anirban Banerjee 13 Feb '18

13 Feb '18

There is an open postdoctoral position for a membrane protein structure-function project in my lab at the NIH. We are currently focusing on integral membrane enzymes (Science. 2018, doi: 10.1126/science.aao6326) and transporters of transition metal ions (J Biol Chem. 2018, doi: 10.1074/jbc.M117.817478). Here is the formal announcement - EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT, BETHESDA, MD AND SURROUNDING AREA Position Description: The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We combine structural techniques such as macromolecular crystallography with biophysical and biochemical methods such as reconstitution based assays, high resolution microscopy and small molecule screening to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. Our laboratory is part of the Cell Biology and Neurobiology Branch in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). We also have an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). Qualifications: The candidates should hold a Ph. D. degree, be author of at least one first author publication and have a strong background in biochemistry or structural biology. Experience with basic molecular biology, protein expression, purification and biochemical characterization are required. Prior experience in membrane protein biochemistry or mammalian expression system for protein purification will be added advantages. It is absolutely essential the candidate is motivated and prepared to put in the best efforts for fruition of the project goals. We are a small, friendly lab and ability to work as part of a cohesive group is important. To Apply: Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests. The NIH is dedicated to building a diverse community in its training and employment programs.

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how to inhibit selectively undue H....O repulsion during refinement with phenix.refine ?
by Maxime Cuypers 10 Feb '18

10 Feb '18

Hello, i am refining neutron data with hydrogens on water molecules complexes that systematically bounce the whole molecule away from the hydroxyls or carboxylic groups or other waters. the Fo-Fc map is crystal clear about where the H atoms should go... any commands i can enter in i.e. a .param file to inhibit repulsion and promote closer h bonds? thanks for your help, cheers, Dr. Maxime Cuypers Post-Doctoral Research Associate, Structural Biology St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA

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query re local grid search in phenix.real_space_refine
by Oliver Clarke 10 Feb '18

10 Feb '18

Hi all, Related to the last message - when using local_grid_search, does phenix attempt to torsion-angle search every residue, or just outliers? It would seem like maybe using EMRinger or similar to identify residues where there is strong sidechain density, but in a non-rotameric position or with an incorrectly fit rotamer might be one way to make it more efficient if it is the former. I don’t want phenix trying to do a local grid search on residues with no sidechain density - these may be in an area of the map with poor local resolution, perhaps where I have docked a crystal structure, or carefully manually adjusted rotamers - local grid search in these regions is likely to make things worse if it is not focused on residues with clear sidechain density. Cheers Oli

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parallelization of local_grid_search in phenix.real_space_refine?
by Oliver Clarke 10 Feb '18

10 Feb '18

Hi all, phenix.real_space_refine runs pretty decently with run=minimization_global+adp, and the adp part is already parallelized. Using local_grid_search though, it slows down enormously, particularly for large structures, and I’d really like to try using it to correct poorly fit rotamers. Is there any prospect for parallelizing this function? Naively it seems like something that might be amenable to parallelization - so long as adjacent local grids aren’t searched at the same time, it would seem like one might be able to split up the job to run on multiple threads? These days a lot of folks have GPU workstations for cryoEM, which often (in addition to GPUs) have Xeon or Threadripper CPUs with many cores - I’d love to be able to use that computational horsepower effectively for refining my structures. Cheers Oli

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Phenix.molprobity PDB pre-test
by Rune Thomas Kidmose 09 Feb '18

09 Feb '18

Hi, After using Phenix.molprobity I noticed it does a test of the input PDB file in the beginning, where it, among other things, identifies duplicate atom labels and then proceeds to list some of them (and hides the rest some where I guess). It also identifies mismatches between the atom label and the atom type, e.g. if a CB is by mistake listed as an O instead of a C, in the last column in the PDB file. I would like to know if it is possible to somehow call this PDB pre-test function used within phenix.molprobity? or maybe something similar in the phenix package? I would like to use the feature in a small MD pipeline I am developing where the input PDB files are checked for duplicate atoms and mismatches between atom label and type. I believe something like the mentioned pre-test feature would work much better, than my current bash script solutions using combinations of awk, grep, sort, uniq etc. Cheers Ruki

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clashscore
by 潘晓伟 09 Feb '18

09 Feb '18

Hello everyone I refine a cryo EM data with 3.1 angstrom, the model fit well with the map, but the clashscore is high, abot 23. How can I decrease the value of clashscore with realspace.refinement in Phenix GUI. Thanks! Pan ________________________________ xiaowp82(a)hotmail.com

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Computational Crystallography Newsletter, Volume 9, Number 1
by Nigel Moriarty 08 Feb '18

08 Feb '18

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. January 2018 <http://phenix-online.org/newsletter/CCN_2018_01.pdf> Articles - Cβ deviations and other aspects in Amber versus CDL refinements <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=21> - A few benchmark tests of various compilers on Linux and Windows <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=25> Short Communications - Tools for model-building with cryo-EM maps <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=7> - Gemmi – a new MX library <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=13> - Overfitting to Ramachandran and geometry criteria in the cryoEM Model Challenge <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=16> Fitting tips #15 – New help to make your 2.5–4Å cryoEM structure even better <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=2> FAQ - What happens when the Phenix GUI prompts me to send an error report? <http://phenix-online.org/newsletter/CCN_2018_01.pdf#page=6> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Residual B values after refinement
by ANAN YUENYAO 07 Feb '18

07 Feb '18

Dear All, I have encountered some error during the PDB validation process after refinement with PHENIX (1.13). After uploading the coordinates and structure factor file, in the header 'Basic coordinate validity', it says that the data contains residual B values. Could anyone please explain the reason behind this error message. Is it going to be problematic for the future PDB deposition? P.S. I have already performed TLS and group B-factor refinement. Thank you in advance! Anan

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FASTA format for sequence file
by egoers＠uoregon.edu 06 Feb '18

06 Feb '18

Hello, I'm trying to run Phase-MR on Phenix (older version) and having trouble formatting my sequence properly. I keep getting error "Protein Sequence not recognized in Composition". I have a good idea of what FASTA should look like (carrot with a name, no spaces or weird characters, followed by the sequence in all capital letter on the next line). I have tried many things, mainly using gedit and plain text files (.txt). I've made sure the file name doesn't have any strange characters as well. If I cut and paste a FASTA file from the PDB into gedit, save that at a .txt, Phaser accepts it. If I cut and paste my protein sequence into the same file, it rejects it. Suggestions?

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how to bypass/deactivate dictionnary check for restraints in phenix.refine
by Maxime Cuypers 02 Feb '18

02 Feb '18

Hello All, I am refining an unusual complex moiety in a protein xl with neutron data. Does anyone know if it is possible to bypass/deactivate dictionnary .cif check i got the blocking error message "it looks like angle and bond restraints are conflicting." and Phenix.refine stops. but really it s not conflicting: my .cif file works great in coot to model the complex. it is hydrogen based, so i really need restraints to get it optimal. any clues welcome, many thanks in advance. Dr. Maxime Cuypers Post-Doctoral Research Associate, Structural Biology St Jude Children s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105-3678, USA

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side-chain on special position.
by Aaron Oakley 02 Feb '18

02 Feb '18

Hello fellow Phenix-ers, I have a structure I am trying to finish in Phenix.refine The is one problem: a glutamate residue sitting on a crystallography 2-fold axis with partial occupancy (picture attached). This residue and its symmetry mate appear to take turns sitting at this position: filling the density leads to severe collision with its symmetry mate. Building the side-chain with occupancy 0.5 doesn’t seem to help, as the residue is pushed out of density during refinement. Any work-arounds? Thanks all, Aaron [cid:[email protected]]

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phenix auto sharpen local sharpening masking artifacts?
by Oliver Clarke 01 Feb '18

01 Feb '18

Hi, I’m trying to run phenix.auto_sharpen with local sharpening, because I have an EM map that has a reasonably substantial variation in local resolution. This is the command I used: phenix.auto_sharpen cryosparc_exp001049_008.mrc resolution=3.26 local_sharpening=true local_aniso_in_local_sharpening=true model.pdb nproc=4 seq_file=seq.fasta >& log & The resulting map looks beautiful (maybe a little too beautiful??) around the model, but shows some funky looking masking artifacts in the density further away from the model (in the micelle region) - see screenshot. Am I doing something wrong? And can I trust that the density is completely free of model bias? Cheers Oli

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Unwanted LINK Records
by Whitley, Matthew J 26 Jan '18

26 Jan '18

Hello all, I am currently refining a structure using Phenix 1.13-2998. Present in this structure is a diphosphate-containing ligand. In the protein chain surrounding the binding site, there is an arginine side chain that points generally toward the diphosphate group, but I cannot define the specific location of the side chain because the side chain density is very poor. The density for the ligand is unambiguous. Upon refinement, Phenix places the Arg side chain so close to the ligand that it draws a covalent bond between the two, and the post-refinement PDB file contains a LINK record for this bond. In reality, the two are not covalently connected, and ideally Phenix would find a conformation for this side chain that is outside of covalent bonding distance. I have tried refining after manually moving the side-chain to a non-clashing position multiple times, but in every case the output PDB contains a LINK for a covalent bond between ligand and side chain. My question: How can I tell Phenix NOT to allow these atoms to come with covalent bonding distance? Is there some kind of "anti-LINK" information I can feed it that will force phenix.refine to select some other conformation for the side chain? Thanks for your advice. Sincerely, Matthew Whitley --- Matthew J. Whitley, Ph.D. Research Instructor Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine

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Open Research Positions: Structural Biophysics of Protein Allostery, in New York City
by Daniel Keedy 26 Jan '18

26 Jan '18

The Daniel Keedy Lab at the ADVANCED SCIENCE RESEARCH CENTER (ASRC) AT CUNY in New York City has available positions for a POSTDOCTORAL SCHOLAR and a LABORATORY TECHNICIAN starting in 2018. The lab’s goal is to elucidate the role of protein flexibility in allosteric regulation — and to use that knowledge to control the function of dynamic, biomedically important enzymes such as tyrosine phosphatases. To do so, we combine cutting-edge experimental and computational techniques in structural biology, including multitemperature X-ray crystallography, high-throughput protein:ligand structure determination, and new algorithms for modeling alternative protein conformations based on electron density maps. REQUIREMENTS FOR THE POSTDOCTORAL SCHOLAR POSITION: a PhD in structural biology, biophysics, computational biology, or a related field; multiple years of experience studying proteins or other macromolecules; and excitement to try new techniques at both the bench and the keyboard. Familiarity with X-ray crystallography, a programming language, and the command line are preferred. REQUIREMENTS FOR THE LABORATORY TECHNICIAN POSITION: an MS, BS, or similar degree in biochemistry, molecular biology, or a related field; experience conducting research in a laboratory setting; and excellent organizational and communication skills. Experience with cloning, protein purification, and/or X-ray crystallography are preferred. OFFICIAL APPLICATIONS: For the postdoctoral scholar position, please apply here: https://cuny.jobs/new-york-ny/research-associate-structural-biology-advance… For the laboratory technician position, please apply here: https://cuny.jobs/new-york-ny/research-assistant-laboratory-technician-stru… ABOUT THE ASRC: The ADVANCED SCIENCE RESEARCH CENTER (ASRC) at the Graduate Center of the City University of New York (CUNY) elevates scientific research and education at CUNY through initiatives in five distinctive, but increasingly interconnected disciplines: STRUCTURAL BIOLOGY, NANOSCIENCE, PHOTONICS, NEUROSCIENCE, and ENVIRONMENTAL SCIENCES. The ASRC promotes a collaborative, interdisciplinary research culture with researchers from each of the initiatives working side-by-side in the ASRC’s core facilities, sharing equipment that is among the most advanced available. The ASRC is next-door to the cutting-edge inter-institutional NEW YORK STRUCTURAL BIOLOGY CENTER (NYSBC), and is also just 70 miles from the newly-constructed NATIONAL SYNCHROTRON LIGHT SOURCE II (NSLS-II), now the brightest synchrotron light source in the US. — Daniel A. Keedy, Ph.D. Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry and Chemistry Ph.D. Programs, CUNY Graduate Center http://www.keedylab.com // daniel.keedy(a)asrc.cuny.edu<mailto:[email protected]> // 212-413-3246

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Amber force field for phenix.real_space_refinement?
by Sebastian Eustermann 24 Jan '18

24 Jan '18

Dear All, I just wondered whether/how one can use the Amber force field also for phenix.real_space_refinement? I tried “use_amber=True” as it is implemented for phenix.refine but that option does exists for phenix.real_space_refinement … Thanks for your help BW Sebastian -------------------------------------- Sebastian Eustermann, PhD Gene Center LMU Munich, Germany

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phenix.auto_sharpen expected filtration of input map
by Ricardo Righetto 24 Jan '18

24 Jan '18

Hi, So far I have liked very much the results of phenix.auto_sharpen, but one thing is not yet clear to me: how does it expect the input map to be filtered? Would be something like: a) Unsharpened, unfiltered map (e.g. the simple average of the half-maps) b) Unsharpened, SSNR-weighted (Cref) (Rosenthal & Henderson, JMB 2003) c) Doesn't matter / other? Thanks in advance! Best wishes, -- Ricardo Diogo Righetto

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Error with Phenix refine after adding ligand
by Mian-Chee Gor 23 Jan '18

23 Jan '18

Hello all, I run into this problem when I tried to refine my protein structure after adding ligand. The ligand that I am adding is a malonate, and the 3-letter chemical code is MLI. I add the ligand using Coot and it fit perfectly into the electron density map. I then tried to run phenix.refine by giving the protein structure pdb file, the original mtz file and the protein sequence fasta file. However, there was an error message saying missing restraints for the ligand. So I generate the CIF file for the ligand using the Ready Set icon in the toolbar. The ligand CIF file and a updated protein structure pdb file was generated and automatically added to the refinement windows. However, when I run the refinement, I saw this error message: Number of nonbonded interaction distances <0.001:2. Please inspect the output above (or in the log window) and correct the input model file. When I inspect the log window, the error is due to the oxygen atoms in the ligand being too close to each other. Why is there an error if the ligand was generated automatically in Phenix? Has anyone encounter this problem before? How do you solve that? Many thanks in advance! -- Dr Mian-Chee Gor Research Fellow Griffith Institute for Drug Discovery (GRIDD) Don Young Road, Nathan, QLD 4111 Mobile: +61 4 2084 7785 Email: m.gor(a)griffith.edu.au

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Neutron diffraction protein refinement with Phenix
by Rex Palmer 22 Jan '18

22 Jan '18

I would like to contact someone based in or near London whois familiar with Phenix refinement of neutron diffraction protein structures and interpretation of the results. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4641-3954-7

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secondary structure presentation in VMD
by CPMAS Chen 22 Jan '18

22 Jan '18

Hi, Phenix users, This may be a little off-topic. I have posted this in VMD users mail list. I want to try here too to see if anyone experienced similar issue. VMD and pymol gave different presentation on the secondary structure of a protein. During phenix.refinement, I added secondary structure restraints and correctly labelled all helices and sheets. However, VMD does not correctly present the secondary structure in cartoon/new-cartoon presentation. A little more detail. In VMD-1.9.4a12, after I loaded the pdb, I chose new cartoon to present the secondary structure. All chains are presented as random coil, the same as tube representation. However, pymol correctly shows the secondary structure of the same pdb file in cartoon representation. Has anyone encountered similar situation? what would be the fix? Thanks! Best Regards, Charles -- *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Refining a neutron structure
by Rex Palmer 19 Jan '18

19 Jan '18

When refining a neutron structure with Phenix why would the program appear to think it was an X-ray structure? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4641-3954-7

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XChem compound design: recruiting programmer / software engineer
by Frank von Delft 19 Jan '18

19 Jan '18

Dear MXers We are recruiting a software engineer (or scientific programmer, or geek-minded scientist, or scientifically-minded geek) to help us get a lot better at designing compounds from hits from crystallographic fragment screening. The post is linked to the XChem facility <http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html> at Diamond's beamline I04-1, set up in partnership with the SGC-Oxford, which is now routinely hosting users every week, allowing them to find convincing fragment hits with a few days' worth of experiments. In 2017, over 30 users measured over 35,000 crystals in academic and industrial XChem experiments. To confront the next bottleneck, namely converting low potency fragments into high-potency compounds, we are setting up a suite of easily accessible computational tools that streamline the obvious yet surprisingly fiddly analyses by which to identify the most sensible follow-up compounds that are easy to make or procure. The (initially) two-year post will, in a team of three and depending on interests, build infrastructure, harden existing algorithms or help evolve new ones, do web interface design, or any combination of the above. The project is seeding a nascent effort, for now aspirationally code-named CCP-CMC (/CompMedChem/, http://www.ccp-cmc.org/), to bring the awesome collaborative ethos of CCP4 and other MX tools to computational medicinal chemistry. Recruitment details are here <https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.disp…>. Deadline is Monday 29 Jan (it's wrong in the link). -- Prof Frank von Delft Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile) Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F)

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