- phenixbb - phenix-online.org

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

08 Sep '16

Dear community, I would like to count crystal contacts bewteen ASU and symmetrics along the cell axis (a, b, c). Could someone point to me a way to do this? Thank you very much in advance. vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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Phenix validate without map/mtz?
by Oliver Clarke 07 Sep '16

07 Sep '16

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

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Data processing
by Sharan Karade 07 Sep '16

07 Sep '16

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

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

06 Sep '16

Dear all, a post-doctoral position is available in the research group of Associate Prof. Maike Bublitz at the Department of Biochemistry, University of Oxford. The project aims to understand the structure and function of microbial membrane transport proteins identified as potential new drug targets, using a combination of state-of-the-art structural (X-ray crystallography, cryo-EM) and biochemical/biophysical techniques. Applicants should hold a PhD in a relevant subject area, such as membrane protein biochemistry or structural biology. Experience in native or recombinant membrane protein expression, purification and either structural determination or functional analysis using biochemical and biophysical techniques is essential. Ability to work in a team as well as contribute to supervision activities and excellent verbal and written communication skills are expected. Experience in protein X-ray crystallography and/or cryo-EM is an advantage. To apply for this role and for further details, including the job description and selection criteria, please click on the link below: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Applications for this vacancy are to be made online by 14th September 2016. PLEASE NOTE: THIS IS A READVERTISEMENT, PREVIOUS APPLICANTS NEED NOT APPLY. Best regards, Maike ************************************************* Dr. Maike Bublitz Associate Professor of Microbial Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom phone: +44 (0)1865 613221 maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk> ************************************************* Dr. Maike Bublitz Associate Professor of Microbial Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom phone: +44 (0)1865 613221 maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk>

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Computational Crystallography Newsletter, Volume 7, Number 2
by Nigel Moriarty 30 Aug '16

30 Aug '16

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. July 2016 <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf> Articles - Working with EIGER data <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=11> - Processing XFEL data with cctbx.xfel and DIALS <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=18> Short Communications - Using Molecular Dynamics Simulations to Enrich the Water Structure in Biomolecular Crystals <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=7> Fitting tips #12 – Twist Tells: better β strands at >3.5Å in x-ray or cryoEM <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=2> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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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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