- phenixbb - phenix-online.org

Phenix.refine peptide chain break
by Booe, Jason M (HSC) 29 Jul '16

29 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

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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

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Phenix download issues
by Billy Poon 25 Jul '16

25 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

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Fall 2016 MicroED workshop at Janelia Research Campus (Reminder)
by Hattne, Johan 21 Jul '16

21 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

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Berkeley Server Downtime (24 hours, 7/22 - 7/23)
by Billy Poon 20 Jul '16

20 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

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MolProbity C-beta outliers
by Yufan Wu 18 Jul '16

18 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

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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

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Amber in phenix
by R. Gasper-Schönenbrücher 12 Jul '16

12 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

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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

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Question about restrain of a nonstandard peptide
by Yufan Wu 05 Jul '16

05 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

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Glycan refinement in Phenix.real_space_refine
by Simonas Masiulis 05 Jul '16

05 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

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.cif file created by Jligand for used in phenix.model_vs_data
by luzuok 05 Jul '16

05 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

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iNEXT news
by Anastassis Perrakis 05 Jul '16

05 Jul '16

Dear all, A new access modality has now been open in iNEXT (http://www.inext-eu.org <http://www.inext-eu.org/>) "From macromolecular sample to X-ray data collection” This novel access modality, hosted at the EMBL Hamburg and Grenoble Units, will provide transnational access to hands-on assistance for sample characterization and crystallization trials, leading to structural data via X-ray crystallography and/or solution small angle scattering. The users are expected to have a macromolecular sample that has already underwent some initial characterisation, and ideally to have performed initial crystallisation trials with promising results. If users cannot obtain such data in their home laboratory, they can first request a 'Structural Audit' via iNEXT. This modality can provide a report that can be automatically included to this application for pushing the project forward towards obtaining more extensive structural data. Successful "Structural Audits" will be fast-tracked towards extended support via this or other modalities. Please do note, that a small proportion of iNEXT access modalities is also open for non-European users, other than the countries listed in our web site. We also want to remind you that most iNEXT access modalities are now open: Structural Audit (sample mail-in for quality assessment for structural biology studies or SAXS-only characterisation) Mail-in characterization of a macromolecular sample, including stability, oligomeric state, crystallization and SAXS; also NMR and negative stain EM for suitable samples. Enhanced Support (Dedicated expert help for specific structural biology projects) From macromolecular sample to X-ray data collection Hands-on assistance for sample characterization and extensive crystallization trials, leading to structural data via crystallography solution and/or small angle scattering. Cryo-EM sample optimisation Hands-on assistance in optimizing a sample for single particle EM; a good quality preliminary characterization by negative stain is the minimal entry point. Macromolecular interactions Hands-on assistance for quantifying the steady state and transient kinetics underlying macromolecular interactions, by fluorescence methods, MALLS, SPR, ITC, MST High-end Data Collection (For experts: access to high-field NMR, X-ray and high-resolution EM equipment) Synchrotron data Access to synchrotron beamlines for X-ray Crystallography and/or SAXS, for translational research project(s); for single or multiple visits and research groups. High-field NMR Access for experienced NMR-scientists to visit host institutes for acquiring solution or solid state NMR spectra on high-field instruments. High-resolution EM Access to state of the art electron microscopes for single particle, tomography and correlative light and electron microscopy (CLEM). A specific note for synchrotron data applications: projects can request multiple visits for a combination of MX, SAXS, and remote access in multiple sites, and the access can be split in several visits. A “project” should have a scientific theme of translational value, but is not necessarily limited to a specific ’target'. Multiple macromolecules and complexes can be pooled under the same proposal, as long as the research theme can be described in a concise and consolidated manner, with clear statements about availability samples and the reasoning behind specific experiments. "Structural Audit" or "From macromolecular sample to X-ray data collection"? Structural Audit contains basic crystallisation screening, MALLS and SAXS; if you already have such data, we recommend that you proceed to the Enhanced Support. Please do note however, that labs with strong experience in the field, should preferably aim for the High-end Data Collection; these modalities are aiming to help labs new to X-ray studies. Please also note that these are not similar to the old Biostruct-X requests for access to crystallisation facilities only, but are meant to be accessed as a coherent package. Please note that "Structural Audit” review is very rapid and the experiment contains no physical presence, so the application and experiment turnover can be rapid. For questions about X-ray methods please mail me; for NMR and EM related questions please mail Hans H.L.J.Wienk.AT.uu.nl Best regards, Tassos

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Post-doctoral position in membrane protein structure and function, University of Oxford, UK
by Maike Bublitz 22 Jun '16

22 Jun '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 18th July 2016. Informal enquiries can be sent to maike.bublitz(a)bioch.ox.ac.uk<mailto:[email protected]>. 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>

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Just before crystallographic structure deposition
by cedric bauvois 22 Jun '16

22 Jun '16

Dear all, At the end of model-building, several modifications are often required for submission (remove some water molecules, deal with unusual bad bond, ...). After doing so, is there any way in phenix to generate a new pdb file containing updated informations (r_factors, bonds, angles, model content,...) ? Thanks a lot Cedric

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Deadline for registrations for the GRC on Diffraction Methods in Structural Biology is this Sunday.
by Edward Snell 16 Jun '16

16 Jun '16

Last chance to register for the Gordon Research Conference on Diffraction Methods in Structural Biology to be held at Bates College in Lewiston, Maine, July 17th-22nd 2016. The conference is themed around "Probing the structure and dynamics of macromolecules" and details of the program are at https://www.grc.org/programs.aspx?id=11655. The closing date for applications is this Sunday June 19th. Please join us in Maine this summer for the 40th anniversary of this meeting. Eddie Snell and Arwen Pearson Edward Snell Ph.D. CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Heisenberg was probably here!

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Project Scientist positions for computational methods
by Nicholas Sauter 13 Jun '16

13 Jun '16

Two Project Scientist positions are available in my group in the *Molecular Biophysics and Integrated Bioimaging* <http://biosciences.lbl.gov/divisions/mbib/> (MBIB) Division at Lawrence Berkeley National Lab. *Bioimaging Project Scientist* Position Summary: We have an exciting opportunity for a Bioimaging Project Scientist who will apply neuromorphic computing techniques to structural biology problems in X-ray diffraction, CryoEM, and CryoET. This will be a cross-disciplinary effort between MBIB and the Computational Research (CRD) Division at Lawrence Berkeley National Laboratory. The research group will include investigators Nick Sauter (X-ray Crystallography), Karen Davies (CryoEM/ET), and Chao Yang (Scalable Solvers). Specific Responsibilities: - Investigate how to apply deep learning algorithms to specific data processing and data interpretation problems in structural biology. - Implement convolutional neural network (CNN) code on neuromorphic computing hardware such as the IBM TrueNorth chip. Example problems include the identification of positive diffraction events in X-ray free-electron laser diffraction, conformational classification in CryoEM single particle reconstruction, and the identification of 3D sections for CryoET subtomogram averaging. - Use tools such as MatConvNet, CAFFE, THEANO or TensorFlow to construct and train CNNs that can be used to optimally classify experimental data. Required Qualifications: - Research experience in Structural Biology, with expertise in allied fields such as Bioinformatics, Mathematics, Computer Science, or Engineering (Ph.D. + 3 years or equivalent) - Strong background in image analysis and machine learning, including neural networks. - Working knowledge of image classification and/or other image processing techniques. - Proficient programming skills in MATLAB and/or Python. - Working knowledge of performance optimization for scientific codes. *Algorithm Developer Project Scientist* Position Summary: We are seeking an algorithm developer for the increasingly complex analysis of large diffraction datasets in structural biology. Current projects utilize XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting and to probe other metalloenzyme reactions. We also wish to test whether diffuse scattering can reveal correlated atomic motions in crystals. Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals. Our software development projects (including packages such as DIALS <http://dials.lbl.gov/> and cctbx.xfel <http://cci.lbl.gov/xfel>) have been highlighted in several high-impact publications listed HERE <http://biosciences.lbl.gov/profiles/nicholas-sauter>. Specific Responsibilities: - Continue work on the DIALS data integration suite. - Test new algorithms for optimally characterizing and merging data from serial crystallography experiments. - Analyze anomalous scattering from metalloenzymes using XFEL diffraction. - Investigate whether diffuse scattering can reveal correlated atomic motions in crystals. Required Qualifications: - Expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction, Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods. - Extensive data analysis experience in crystallography or from more general bioimaging backgrounds are welcome. - We particularly encourage strong mathematical intuition and a track record of bringing new ideas and tools to fruition, as evidenced through written publication and clear presentation. Candidates should send an expression of interest, CV, and list of three references to Nick Sauter, nksauter(a)lbl.gov*. *Further details are posted at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82554. Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

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Post-doctoral position in Structural Biology
by Dhirendra K Simanshu 13 Jun '16

13 Jun '16

A post-doctoral position ( structural biology) is available in the RAS initiative at Frederick National Laboratory for Cancer Research (operated by Leidos Biomedical Research for NCI) . Please visit the link below for more details and instructions on how to apply: http://jobs.leidos.com/ShowJob/Id/861827/Post-Doctoral-Fellow-629153-(NCI)/ *JOB DESCRIPTION* The structural biology group in the RAS initiative focuses on structural analysis of KRAS mutants and biologically relevant KRAS activator/effector complexes in support of drug discovery efforts and to further understand the biochemistry of RAS proteins. We are looking for a highly motivated post-doctoral fellow to join our group. Highly motivated candidates who recently obtained a Ph.D. with a strong background in biochemistry, biophysics and structural biology are encouraged to apply. This post-doc will work closely with the protein production group and carry out structural studies on oncogenic KRAS complexed with effectors, GAPs, regulators and small molecules. We use X-ray crystallography, NMR, molecular modeling, and other biophysical techniques for structural characterization. The candidate will be expected to be able to participate in experimental design and to independently conduct experiments in a priority-driven environment. The candidate should have the ability to act both independently and as a part of the RAS team in pursuit of specific research goals and objectives. The structural biology group in the RAS initiative works very closely with the biochemistry and biophysics group, and is well equipped with crystallization robotics, in-house X-ray generator, and has regular access to the synchrotron beamline at Argonne. *Qualifications:* BASIC QUALIFICATIONS - Possession of a doctoral degree from an accredited college/university according to the Council for Higher Education Accreditation (CHEA) in a field related to structural biology, biochemistry, biophysics or computational biology - Foreign degrees must be evaluated for U.S. equivalency - Demonstrated proficiency in protein biochemical and biophysical characterization - Ability to act both independently and as a part of the RAS team in pursuit of specific research goals and objectives - Ability to conduct experiments and evaluate results independently - Experience in crystallization and structure determination of protein-ligand and protein-protein complexes PREFERRED QUALIFICATIONS - Experience working with small GTPases or RAS-related effector proteins and Knowledge of molecular dynamics simulations and protein-ligand docking.

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Diffraction Methods in Structural Biology GRC - Last chance to register
by Edward Snell 10 Jun '16

10 Jun '16

Dear Colleagues, The registration deadline for this year's Diffraction Methods in Structural Biology GRC (17-22nd July 2016) held in Maine, USA is rapidly approaching (19th June). This year will be the 40th Anniversary of this GRC and we have a cracking program (or programme) for you (http://www.grc.org/programs.aspx?id=11655) including talks on new beamlines and sources, as well as presentations of many new tools (experimental and computational) for getting more information out of your data. There is also the traditional Thursday morning session (for which talks are selected from posters at the meeting itself) that will feature the latest and most exciting developments in diffraction methods So if you have something really cool you'd like to present, there is still time to apply! If that wasn't enough to tempt you, the main meeting will be preceded by a 2 day Gordon Research Seminar (16-17th July, http://www.grc.org/programs.aspx?id=16486) arranged *by* students and postdocs *for* students and postdocs. We strongly encourage and invite students and postdocs to attend and then come to the full meeting immediately afterward. We look forward to seeing you in July. Best wishes Eddie Snell & Arwen Pearson Edward Snell Ph.D. CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Heisenberg was probably here!

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Fall 2016 MicroED workshop at Janelia Research Campus
by Hattne, Johan 08 Jun '16

08 Jun '16

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

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twinning detection
by Ursula Schulze-Gahmen 06 Jun '16

06 Jun '16

I have an extremely low resolution data set to 6.5 A. The data were collected on a Pilatus detector, indexed and further processed in XDS, space group P321. Pointless determines spacegroup to P3221 or P3121 and L-test shows no twinning. Phenix X-triage indicates twinning, but the twin fraction varies enormously depending on the method used: Britton analysis 0.337, H-test 0.260, ML 0.022. The UCLA twin server also thinks that data are twinned. How do I evaluate which information is right? Also, I think I found a molecular replacement solution that is correct using these twinned data. Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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GPU acceleration of phenix.real_space_refine?
by Oliver Clarke 02 Jun '16

02 Jun '16

Hi all, phenix.real_space_refine takes a very long time to run on large systems when using any of the more computationally expensive options (e.g. morphing). I was wondering if there has been any consideration towards optimizing this code (and maybe that of phenix.map_to_model) for GPU acceleration? There is somewhat of a shift occuring in the EM community towards using GPU workstations for data processing - if we could use already purchased capabilities to accelerate model refinement as well that would be a huge bonus. I saw a discussion on the bb from a while back concerning the same question applied to phenix.refine, and the conclusion was that in that case the benefits would be minimal, but I'm not sure whether the same applies to real space operations. Cheers, Oli. PS has there been any consideration of including an option to allow users to supply two half maps at run time, one "work" and one "test" map for cross validation purposes? It is possible to do this with two separate runs right now but having the option integrated would be wonderful.

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phenix.real_space_refine GUI
by Pavel Afonine 01 Jun '16

01 Jun '16

Hi Phenix users, since I had to answer this very same question off-list three times in past 48 hours, I thought I post this for future reference... Yes, thanks *Billy* there is a GUI for phenix.real_space_refine (tool to refine atomic models against maps, such as cryo-EM maps)! To give it a try, you need: 1) Get the latest nightly build, dev-2427 for instance: http://phenix-online.org/download/nightly_builds.cgi 2) Enable alpha-test programs in Phenix GUI. To do this: -- start Phenix GUI; -- go to Preferences and tick "Enable alpha-test programs and features" box; -- restart the GUI (close down, then start again); -- phenix.real_space_refine will be available in Refinement section on the right (Real-space refinement [alpha]). Note, it has a very handy feature to see/explore/edit secondary-structure restraints graphically. Also note that *this is alpha-test version meaning that glitches are not unexpected*! However your feedback will help to improve it, so please let us know should you encounter problems, have suggestions or found bug(s)! All the best, Pavel

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r-free flag cell constant mismatch
by wtempel 01 Jun '16

01 Jun '16

Dear Phenix experts, our project involves crystals *A* and *B*, which are nearly isomorphous and of a protein’s complexes with two different small molecules, respectively. *A* diffracts better than *B*. The r-free flag from *A* was “attached” to *B*‘s input reflections with the CCP4 cad command and is still associated to *B*‘s slightly different cell dimensions. Would/should this be reason enough for refine to throw an error? The error message suggests changing the refinement.input.symmetry_safety_check setting. Can this setting be changed in the GUI? Thank you. Wolfram Tempel

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Berkeley Server Downtime (6/3/2016)
by Billy Poon 01 Jun '16

01 Jun '16

Dear all, On Friday, June 3, our servers will be shutdown starting at 6:30 am Pacific for scheduled maintenance in our building (7 - 8 am). 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/) We expect that the servers will be available by 8:30 am Pacific at the latest. 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

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