- phenixbb - phenix-online.org

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

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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.

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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

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Merged data for "Table 1"
by Yufan Wu 10 Aug '16

10 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

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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

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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 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

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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 14 Jun '16

14 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 09 Jun '16

09 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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Gordon Research Conference on Diffraction Methods
by Edward Snell 01 Jun '16

01 Jun '16

While not a Phenix posting, we do encourage attendance from the usual suspects! We'd like to remind you to register for the Gordon Research Conference on Diffraction Methods 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 June 19th 2016, about 5 weeks away, however GRC conferences have a limited number of participants and we will close registration early if that number is reached. Please join us in Maine this summer for the 40th anniversary of this meeting. If you are planning on attending, please note the deadline, and the growing potential that registration may close earlier. Thanks, Eddie Snell and Arwen Pearson - Chair and co-chair for 2016. 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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rosetta_refine connecting non-consecutive residues around break in chain
by wtempel 27 May '16

27 May '16

Hello, can one prevent rosetta_refine from connecting two residues that surround a gap? For example, how do I keep near-by residues 108 and 115 apart when 109 through 114 are missing? Thank you. Wolfram Tempel

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Fwd: Re: Scultor model with gaps included
by Gabor Bunkoczi 26 May '16

26 May '16

Apologies, this should have been directed to the mailing list. Gabor -------- Original Message -------- Subject: Re: [phenixbb] Scultor model with gaps included Date: 2016-05-25 14:33 From: Gabor Bunkoczi <gb360(a)cam.ac.uk> To: Joseph Brock <joseph.brock(a)ki.se> Dear Joseph, apologies for the late response, and sorry for the trouble. Please find some answers inlined. On 2016-05-24 15:10, Joseph Brock wrote: > Dear Phenix community, > > I was hoping if someone could help me with using Phaser correctly, > since I can't seem to produce the desired search model. > > The first thing that I was wondering about is that the CLUSTAL > alignment from the log file is quite different to the .aln alignment I > made with phenix --> other tools --> multiple sequence alignment. Why > is a sequence alignment required as input if sculptor performs it's > own internally? Sculptor can perform sequence alignment, but the algorithm is relatively basic, and you can get much better results with an external method (such as HHPRED), and hence alignment input is preferred over the target sequence. The alignment selected is printed into the logfile for reference. On the other hand, Sculptor does align the structure of your model chain to the sequence of your model (this is a surprisingly non-trivial task). However, this alignment should be close to 100% identical, unless a mistake has been made (such as using the wrong alignment file). You should get a warning if the sequence identity is too low. It is normally OK to have a couple of mismatches (such as having SeMet in the model structure with translates to "X" and not as "C"). > > My model sequence aligned to my target sequence in the log file has > several gaps in the alignment . For e.g., > > MASTER ......AASFIMV...... > CHAIN_A ......AKM--MF....... > > I would like to great a search model in which the residues aligned to > gaps in the MASTER chain are included, however the resulting sculptor > .pdb file has these residues removed. Shouldn't they be inserted so > that the rest of the chain is in the correct register? You need to do homology modelling to achieve this, as an insertion can affect the whole structure. Sculptor is designed for quick model improvement, and just renumbers/renames residues. However, the new residues numbers should reflect your sequence, i.e. in your example alignment the two methionines on both sides of the gap will get a non-consecutive number and are displayed as non-bonded in e.g. Coot. > > If anyone can let me know the parameters to allow this, I would > greatly appreciate it. I tried unselecting 'gap' in main-chain > deletion scope and some other variations, but this didn't seem to > help. > > I seem to get the same result even if I change the target index from 1 > to 2 in the associated .aln alignment. Does anyone know why this is? Hmm, this does not sound right. Can you send me the logfile so that I can have a look (please use my direct email address)? Best wishes, Gabor > > Apologies if this is quite obvious, I have been reading the > documentation but can't seem to figure it out. > > All the best, > > Joseph. > > Joseph Brock | PhD > Division of Physiological Chemistry II > Department of Medical Biochemistry and Biophysics > Karolinska Institutet > Scheeles väg 2 > SE-171 77 Stockholm, Sweden > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org -- ################################################## Dr Gabor Bunkoczi Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital Hills Road Cambridge CB2 0XY ##################################################

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Appropriate model_vs_data usage over part of a structure
by Andy Watkins 26 May '16

26 May '16

Perhaps necessary preface: I am largely learning as I go, and large parts of Phenix (and the details of refinement data file formats) are still black boxes for me. Suppose I have a model of one chain of a complex and an .mtz describing the entire complex. I have performed some refinement procedure altering the model of that single chain. My aim is to determine how this refinement procedure has affected the fit to the experimental data--or, really, the subset of the experimental data expected to be relevant for my model. For obvious reasons, phenix.model_vs_data chain_A.pdb whole_complex.mtz phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz are undesirable: they evaluate the model of a single chain against the whole complex's data, and there's obviously a lot of unsatisfied electron density. So, while this command *works*, it reports an unrepresentative fit. (In theory, one solution to my problem would be to re-combine each chain's refined version, then run model_vs_data on the recombined, refined complex. I'm interested nonetheless in how it would work on the chains separately. Now, during the refinement procedure, we of course generate .ccp4 density maps for the individual chain models: phenix.maps chain_A.pdb whole_complex.mtz which produces the ccp4 file as well as, crucially, chain_A_map_coeffs.mtz. Attempting to employ that resulting .mtz file, i.e. phenix.model_vs_data chain_A.pdb whole_complex.mtz phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz leads to an evocative error: Sorry_No_array_of_the_required_type: No reflection arrays available. My highest suspicion is that I need to alter maps.params in a particular way so that reflection arrays are also output to model_map_coeffs.mtz. I could also imagine that I need to be using another program entirely! Thanks in advance for whatever help you can provide; unfortunately, I can't provide any input files.

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July ACA meeting in Denver early registration still open!
by Terwilliger, Thomas Charles 24 May '16

24 May '16

?Hi Phenix colleagues! Heading to Denver for ACA's Annual Meeting in July? Early registration ends May 31 (abstracts still being accepted too!) See: http://www.amercrystalassn.org/2016-meeting-homepage ?All the best, Tom T Tom Terwilliger (2016 ACA President)

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Scultor model with gaps included
by Joseph Brock 24 May '16

24 May '16

Dear Phenix community, I was hoping if someone could help me with using Phaser correctly, since I can't seem to produce the desired search model. The first thing that I was wondering about is that the CLUSTAL alignment from the log file is quite different to the .aln alignment I made with phenix --> other tools --> multiple sequence alignment. Why is a sequence alignment required as input if sculptor performs it's own internally? My model sequence aligned to my target sequence in the log file has several gaps in the alignment . For e.g., MASTER ......AASFIMV...... CHAIN_A ......AKM--MF....... I would like to great a search model in which the residues aligned to gaps in the MASTER chain are included, however the resulting sculptor .pdb file has these residues removed. Shouldn't they be inserted so that the rest of the chain is in the correct register? If anyone can let me know the parameters to allow this, I would greatly appreciate it. I tried unselecting 'gap' in main-chain deletion scope and some other variations, but this didn't seem to help. I seem to get the same result even if I change the target index from 1 to 2 in the associated .aln alignment. Does anyone know why this is? Apologies if this is quite obvious, I have been reading the documentation but can't seem to figure it out. All the best, Joseph. Joseph Brock | PhD Division of Physiological Chemistry II Department of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 SE-171 77 Stockholm, Sweden

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Senior Research Assistant position - MD Anderson Cancer Center
by Leonard,Paul 24 May '16

24 May '16

Dear all, This post is to bring your attention to a job opportunity for a Senior Research Assistant position at the University of Texas, MD Anderson Cancer Center (in Houston, Texas, USA). MD Anderson Cancer Center is the number one cancer center in the United States and a center of excellence for both oncology treatment and research. This is an opportunity to join a dedicated team of researchers that are working together to develop new cancer therapeutics to positively impact the lives of our patients. We are looking for a highly motivated individual with experience in molecular biology and protein production to work within our structural biology team to support research projects across the MD Anderson research community and the drug discovery pipeline of the Institute for Applied Cancer Science. The research that stems from the proteins produced has a direct impact on the lives of our patients. Salaries are competitive and based on the level of experience of the applicant. We are looking for applicants with a Bachelors or Masters degree in Biochemistry, Biotechnology, Pharmacology or a related subject. Previous experience working in a research lab environment is desired. The ideal candidate will have previous molecular biology or protein purification experience. For more information and to submit a job application please refer to the job posting… https://mdanderson.referrals.selectminds.com/jobs/sr-research-asst-genomic-… We look forward to reviewing your application. Please use the above link to submit your application, CV and cover letter. Best wishes, Paul Leonard 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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ncs average map
by Jarrod Mousa 21 May '16

21 May '16

Hi all I am trying to use phenix refine to NCS average my density map during refinement. If I check refinement, I get an error saying 'Missing a map type defiinition for one or more CCP4 or XPLOR maps." If I try to upload a 2Fo-Fc map generated from FFT map coefficients, I get an error saying that phenix does not recognize the file. Any tips or other methods to calculate such a map? thanks, Jarrod Mousa

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Postdoc positions at Arizona State Uni: algorithm development for XFEL data
by Nadia Zatsepin 19 May '16

19 May '16

*Open positions: 2 Postdoc positions in XFEL Biophysics at Arizona State University.* Full details & how to apply: *https://physics.asu.edu/about/employment-opportunities <https://physics.asu.edu/about/employment-opportunities>* We are applicants for 2 postdoctoral researcher positions for the development of algorithms for biological X-ray free electron laser (XFEL) data, both in crystallography and solution scattering. The successful applicants will become part of an interdisciplinary team at ASU working on solving important biological questions using XFELs. This is a two-year Postdoctoral appointment with the possibility of extension to a maximum of three years. *Objectives* The objective of these postdoctoral researcher positions is to develop algorithms for improving data accuracy in SFX through modeling and optimization, develop novel phasing methods which exploit the full spatial coherence of the XFEL for 2D and 3D nanocrystals, and/or develop structure-determination methods that can be applied to samples that cannot be crystallized, through XFEL fast solution scattering. *Essential Functions of the position:* - Develop improved algorithms and software for analyzing biological XFEL data (static and time-resolved crystallographic or solution scattering data). - Analyze and present results at conferences, workshops, seminars and technical meetings. - Document and publish research results in peer-reviewed scientific or technical journals. - Contribute to XFEL data analysis workshops organized by the Group The successful candidates are expected to support the analysis of serial femtosecond crystallography experiments at the Linac Coherent Light Source (LCLS), SPring-8 Angstrom Compact free electron Laser (SACLA), the European X-Ray Laser (XFEL), or other applicable x-ray sources (XFELs or 3rd generation synchrotrons). This work is complementary to XFEL data analysis work in the NSF BioXFEL Science and Technology center (STC), and so the candidates will interact and collaborate with students and postdoctoral researchers working in the BioXFEL STC. They will report to the PI for the project. *Required Qualifications:* - PhD in related field such as physics, biophysics, bioinformatics, structural biology, by time of appointment. - Experience in analysis of X-ray diffraction imaging or crystallographic data. - Demonstrated algorithm and/or code development. - Demonstrated publication record in peer-reviewed literature; and experience in presenting research results to large audiences. - Demonstrated ability to perform independent research and in a diverse team environment to achieve program goals in a timely fashion. - Demonstrated fundamental verbal and written communication skills (in English) necessary to work in a multidisciplinary team environment, author technical and scientific reports and publications, and deliver scientific presentations. *Desired Qualifications:* - Experience with X-ray experiments at synchrotrons or XFELs related to high-resolution imaging or crystallography. - Experience and familiarity with coherent x-ray imaging experiments. - Experience with analyzing and solving protein structures. - Demonstrated programming experience in C and Python; experience with , web-interface development - Experience with parallel programming and large data sets. *To apply, *please submit as a single PDF document: (1) a cover letter which includes the names and email addresses of three references, (2) a curriculum vitae with a list of publications. PDF application materials should be submitted via the employment application portal. <https://physics.asu.edu/content/postdoc-position-job-11577-0> *Applications will be reviewed beginning June 15, 2016.* If not filled, every week thereafter until the search is closed. *Anticipated starting date: August 2016. * Please email nadia.zatsepin(a)asu.edu for more information. -- Nadia Zatsepin Assistant Research Professor Dept of Physics PSF246 Arizona State University +1 480 727 6444 nadia.zatsepin(a)asu.edu *http://www.public.asu.edu/~nzatsepi/ <http://www.public.asu.edu/~nzatsepi/>*

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Rfree doesn't decrease and keeps around 36%, High ramachandran outlier, High RMSD
by chen c 13 May '16

13 May '16

Dear all, I am solving a structure which diffracted to 2.8 angstrom resolution and containes 8 molecules (MW:12 kDa) per ASU. It's noteworthy that though the model used for molecular replacement shares 50% sequence identity with my protein, however, severe clashes were found as listed below: Packing Table ------------- Solutions accepted if total number of clashes <= 5% of trace atoms i.e. total number of clashes <= 32 AND if number of clashes <= 5% of trace atoms for each ensemble i.e. ensemble1: number of clashes <= 4 # # #Clash Packs SpaceGroup Annotation 1 17 NO C 2 2 21 ... PAK=11 LLG=802 RFZ=3.8 TFZ=9.3 Only after I changed the packing criteria from 5% to 100%, can I get the solution. Severe clashes and even coincidence of different molecules were found as briefly listed below: Molecule A (C-terminal) vs Molecule D (N-terminal) of neighbouring ASU Molecule B (C-terminal) vs Molecule C (N-terminal) Molecule C (C-terminal) vs Molecule D (C-terminal) Molecule E (C-terminal) vs Molecule G (N-terminal) Molecule F (C-terminal) vs Molecule H (N-terminal) Molecule G (C-terminal) vs Molecule G (C-terminal) of neighbouring ASU Molecule H (C-terminal) vs Molecule H (C-terminal) of neighbouring ASU Upon this, I manually rebuild the structure in COOT and particularly deleted those coincided atoms. Then I refined the structure in phenix. However, all the refine gives a bad result, namely, RMSD(angle) at 1.8-2.1, RMSD(bond) at 0.015-0.02, The Rwork/Rfree at around 0.28/0.36, Ramachandran outlier + Rotamer outlier at around 15-20%. I tried a lot of refinement strategy and the current status is : RMSD(angle)= 1.545, RMSD(bond) = 0.01, Rwork/Rfree = 0.290.36, Ramachandran outlier=11.3%,Rotamer outlier =1.5%. The data set belonged to C2221 and phenix.xtriage analysis reflects no twinning or pseudotranslation problem. In addition, there are two beta-turns in each molecule which displays poor electron density and geometry. And this two loop are the very residues which appears in disallowed regions in ramachandran diagram apart some other residues. However, these residues should have little effect on the R factor considering of their low contribution to the overall structure due to their poor electron density. Has anyone has experiences about this? Your help and advice is greatly appreciated! Thank you! Chen -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:[email protected] 北京市海淀区清华大学生命科学馆201-212室邮编：100084

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occupancy refinement with constrained groups
by Schnicker, Nicholas J 13 May '16

13 May '16

Dear all, I am trying to do use constrained groups with occupancy refinement but struggling with syntax. I am trying to define selection1 as 2 different atoms and selection2 as another 2 different atoms. Therefore I want the 2 atoms in selection1 to have the same occupancy and the atoms in selection2 to have the same and the sum of selection 1 and 2 will be 1. If someone could help me with this syntax I would appreciate it! I have tried using brackets to separate selections but phenix doesn't recognize this. I can provide more information if needed, it's just a complicated scenario. Thanks! Nick

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FreeR flags from AutoBuild
by Sam Tang 13 May '16

13 May '16

Dear all May I enquire a simple question about AutoBuild - I input an experimental data (ccp4 mtz from Aimless) and a model from Phaser-MR to AutoBuild hoping that some mis-fit flexible regions could be re-build. May I know if the output mtz *overall_best_refine_data.mtz* contains the same FreeR flags as in the input, or would AutoBuild generate a new set of FreeR? Or in other words, are the R values directly comparable if I refine against the input experimental data mtz or the overall_best_refine_data.mtz? Thanks! Cheers Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

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FW: [SA_Scat] 4th Annual CCP-SAS Project Meeting
by Kushol Gupta 13 May '16

13 May '16

---------- Forwarded message ---------- From: <stephen.king(a)stfc.ac.uk> Date: Mon, May 9, 2016 at 5:27 AM Subject: [SA_Scat] 4th Annual CCP-SAS Project Meeting To: sa_scat(a)iucr.org Dear Colleagues, We are pleased announce the 4th Annual CCP-SAS Project Meeting to be held at the NIST NCNR, Gaithersburg MD, USA from Mon 23 through Wed 25 May 2016. CCP-SAS includes the SASSIE and SCT suites of 'atomistic' modelling software. The Meeting program is available online at http://www.ccpsas.org/Meetings/Fourth/Program.html This year the Meeting also includes two 'hands-on' Tutorial Sessions on Wed 25 May: one aimed at those who wish to learn how to incorporate additional modules into the SASSIE Framework, and another aimed at those who wish to learn about wrapping applications for Web deployment using GenApp. Registration for the Meeting and Tutorials is FREE, but space is limited and places will be allocated on a first-come, first-served basis. IMPORTANT: As the meeting is being held on the NIST Campus, registration with NIST is mandatory. Please follow the 'Registration' link on the above webpage. Photo ID will be required for entry. There is also the opportunity to present relevant posters on Mon 23 May. Please contact Prof Paul Butler (pbutler(a)utk.edu<mailto:[email protected]>) if you would like to do this. On Tue 24 May there will be a special Workshop for potential future collaborators, software developers, and funders. Attendance at this Workshop is by invitation only. Please also contact Paul Butler (pbutler(a)utk.edu<mailto:[email protected]>) if you might like to contribute to these discussions. We hope you can join us! The CCP-SAS Team

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bug?
by Patrick Loll 12 May '16

12 May '16

I just ran into something that might be a small bug (phenix 1.10.1-2155) Background: I have a problem data set for which the unit cell is too small to hold we thought we were crystallizing (which probably means we crystallized the wrong protein). In any case, I ran the data through Xtriage, supplying the sequence file for the too-large protein, even though I knew this is probably not correct. This sequence file contains 264 residues. I was surprised to see that the program returned with a perfectly reasonable estimate of the Matthews coefficient, making me briefly hopeful that I had been doing the calculation incorrectly. Alas, not so; when I dig through the log file, I find the following: ____begin excerpt_______________________________________________________________ determining composition from sequence file /xxxx/seq.dat Too many residues to fit in the ASU resetting numer of residues in monomer to 26 =================== Solvent content and Matthews coefficient ================== Crystallized molecule(s) defined as 264 protein residues ------------------------------------------------------------------- | Solvent content analysis | |-----------------------------------------------------------------| | Copies | Solvent content | Matthews coeff. | P(solvent content) | |-----------------------------------------------------------------| | 1 | 0.666 | 3.68 | 0.621 | | 2 | 0.331 | 1.84 | 0.379 | ------------------------------------------------------------------- Best guess : 1 copy in the ASU _____end excerpt_______________________________________________________________ So it seems as though the program, when confronted with a protein mass that’s too large for the AU, divides the mass by 10 and tries again. However, this is not clear from the results; in the results section, it states “Crystallized molecule(s) defined as 264 protein residues." So a user might be misled into thinking that everything is OK, when in fact it’s not… Cheers, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

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BCA/CCP4 Summer School 2016 - Applications now open
by Airlie McCoy 10 May '16

10 May '16

I am pleased to announce that applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond Light Source from Sunday 21st August to Friday 26th August 2016 Applications will close Friday 13th May. The registration fee of the school has been kept low due to the generous sponsorship of the BCA and CCP4. Note that up to 10 free places are available to BBSRC funded students. For a draft programme and application details see: http://www.diamond.ac.uk/Home/Events/2016/BCA-Summer-School.html The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP5 programmes will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. (Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines.) We recognise that an active social programme plays a role in enabling students to make links that may be maintained throughout a research career. There will be a conference dinner, and a number of other events, including a boat trip on the Thames from Oxford. Airlie McCoy

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Research Technician Position at Structural Biology Lab at University of Southern California
by Xiao Lei 07 May '16

07 May '16

Dear All, The Lin Chen laboratory at the University of Southern California is seeking a research technician to join the lab. The Chen lab is interested in the structure and function of molecular complexes that control cell signaling and gene expression. We use a multi-disciplinary approach that combines structural biology, chemical biology, biochemistry/cell biology, and computational biology/bioinformatics to study the molecular basis of signal transduction and transcription regulation. For more detailed description of our research, please visit the lab page: http://structure.usc.edu/ Job Responsibilities Include: Assist postdoctoral fellows and graduate students in the lab on a variety of biochemical and biophysical studies, including gene cloning, protein expression, purification, and characterization of purified protein by various biochemical and biophysical techniques, and protein crystallization. The technician may also be involved in developing new techniques to study the structure and function of the genome. The technician is also expected to take a small amount of lab managing duty such as ordering and organizing lab supplies,. Commitment of 1 year is required; 2 years is preferred, the position is grant-funded and renewable Preferred Qualifications: • BS in Biochemistry, or Chemistry, or Molecular Biology, or related field • 2 years lab experience • Working knowledge of laboratory equipment and research protocols • Must be meticulous, detail-oriented, and responsible • Basic biochemistry, molecular biology and chemistry knowledge To apply for this position, Please send CV, three names of reference and a cover letter to: linchen(a)usc.edu Best Regards.

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autoBuild error, OSError: [Errno 12] Cannot allocate memory
by luzuok 07 May '16

07 May '16

Hello, The autobuild had been running for almost 2 hours in my Desktop, but it suddenly stopped and posed an error message as indicated below. Is this caused by my insufficient memory? Best wishes! Luzuokun Splitting work into 4 jobs and running with 2 processors using sh background=True in /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0 Starting job 1...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_4.log Starting job 2...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_5.log Starting job 3...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_6.log Starting job 4...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_7.log Traceback (most recent call last): File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 2372, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 4714, in AutoBuild_rebuild_cycle_run always_reuse_model=always_reuse_model) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 7589, in AutoBuild_build_refine mtz_file=mtz_file,mtz_ref_file=mtz_ref_file) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 7833, in run_standard_build_in_parallel r.run(out=sys.stdout) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/run_group_of_wizards.py", line 294, in run self.start_run(run_file,last=is_last) File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/run_group_of_wizards.py", line 604, in start_run cmd+" "+self.add_double_quote(run_file,escape_space=False)) File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/easy_run.py", line 160, in __init__ close_fds=not subprocess.mswindows) File "/usr/local/phenix-1.10.1-2155/base/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/usr/local/phenix-1.10.1-2155/base/lib/python2.7/subprocess.py", line 1223, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory -- 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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Re: [phenixbb] Self Rotation Function
by Sharan Karade 04 May '16

04 May '16

Thank you for your valuable Edward, Patrick, Francis. I will try with your suggestions. And let you know the results. On 4 May 2016 20:03, "Edward A. Berry" <BerryE(a)upstate.edu> wrote: On 05/04/2016 10:17 AM, Patrick Loll wrote: > You won’t see peaks in the self-rotation function unless the AU contains > non-crystallographic rotational symmetry, which frequently is not the case > (just because you have multiple copies of your protein in the AU does not > imply that they are arranged in any specific, symmetric manner). And even > if there is rotational NCS, if the axis of rotation is parallel to a > crystal symmetry operator, the effect of the NCS will be masked. So > everything may be working as it should. > > If you’re not certain if you have the program working correctly, then I > suggest that you find a structure in the PDB that contains rotational NCS, > download the structure factors, and calculate the self-rotation map, as a > positive control. > > Try bacterioferritin (in a low-symmetry space group) or GroEL ! > On 4 May 2016, at 12:10 AM, Sharan Karade <sharankarade(a)gmail.com> wrote: >> >> Hello everyone, >> >> i am working on data set which has resolution of 2.8 A >> space group C2, the protein have 394 a a . when i estimate Mathews >> coefficient it shows four to five molecules in asymmetric unit. when i try >> to get self rotation function Map by default parameter (10A-3A and 25 >> radius of integration) i was not getting any peak at all 180, 90, 120, 60. >> Or radius of integration affect the results. >> >> Can anybody please help me to sort out with this problem, welcome for >> suggestions, thanks in advance. >> >> -- >> Sharan >> C/O Dr. J V Pratap >> Senior Research Fellow, >> CSIR-Central Drug Research Institute, >> Lucknow >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > > > --------------------------------------------------------------------------------------- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Director, Biochemistry Graduate Program > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pat.loll(a)drexelmed.edu > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > >

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Self Rotation Function
by Sharan Karade 04 May '16

04 May '16

Hello everyone, i am working on data set which has resolution of 2.8 A space group C2, the protein have 394 a a . when i estimate Mathews coefficient it shows four to five molecules in asymmetric unit. when i try to get self rotation function Map by default parameter (10A-3A and 25 radius of integration) i was not getting any peak at all 180, 90, 120, 60. Or radius of integration affect the results. Can anybody please help me to sort out with this problem, welcome for suggestions, thanks in advance. -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

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Phenix.multi_crystal_average
by Sam Tang 04 May '16

04 May '16

Hello colleagues May I enquire if the captioned programme is still supported in the latest version of Phenix and, if not, which programme is now in place for this? Thanks in advance. Cheers Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

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