- phenixbb - phenix-online.org

Phenix version 1.18 released
by Paul Adams 20 May '20

20 May '20

The Phenix developers are pleased to announce that version 1.18 of Phenix is now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that this recent publication should now be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Highlights for the 1.18.2 version of Phenix: 1.18.2 Changes - Fix weighting for iron sulfur clusters 1.18.1 Changes - General bug fixes 1.18 Changes - Amber - Automatic creation of Amber files in phenix.refine GUI - Added AmberPrep GUI - Restraints - Engh & Huber restraints (2001) for cis-peptides now implemented - Restraints added for FeS - Metal coordination library is default to Zn+2 and FeS clusters - Rama-Z: New global Ramachandran score for identifying protein structures with unlikely stereochemistry in CLI (phenix.rama_z, mmtbx.rama_z) and GUI (validation reports). - Density modification for cryo-EM - Includes model-based density modification with automatic model generation - Optimized defaults and additional documentation - Real-space refinement - Hydrogen atoms no longer included in map target function, which improves fit. - Add NQH flip option (enabled by default) - Other - New tool for ordered solvent picking in cryo-EM maps (phenix.douse) - New map and model superposition tool (phenix.match_maps) - New FindProgram to find any Phenix program with a text search - Project details now has a button for opening the README file for tutorials For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Generating a polder map using coordinates
by Petr Kolenko 20 May '20

20 May '20

Dear colleagues, Is there a way to calculate the polder map in a selected box using coordinates instead of atom selection as shown in the "Generating a polder map with the compute_box option" website? Best regards, Petr

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Solving a protein - ligand structure
by Tom Vanmarcke 20 May '20

20 May '20

Dear, We are trying to solve a protein structure that contains a ligand (polyoxometalate). We found the ligand in the electron density but through the middle of the ligand goes a 2 fold axis. For this reason, we placed the occupendency of the ligand on 0.50. When we try to refine the structure using phenix.refine, the ligand breaks down even when adding a cif restrain file. The cif restrain file contains information about atoms, angles and bond lengths. Is there a way to fix this problem? Greetings Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Is there a way to evaluate batch pdb models with Malprobity in phenix?
by Jing Liu 19 May '20

19 May '20

Hi, I had generate a batch of pdb models (40-100) in rosetta and am wondering whether there is a way to evaluate these models in batch with Molprobity. For example, can I use phenix command line to do it and how? Or should I download the Molprobity and do it on my local computer? Really appreciate if anyone can share their experience. Jing Liu, PhD Ted Jardetzky lab Department of Structural Biology Stanford University

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Phenix 1.18 and rotamer outliers
by Xavier Brazzolotto 18 May '20

18 May '20

I’ve installed the latest stable Phenix version (1.18). I’ve noticed a clear difference in the final statistics (MOLprobity) compared to the previous version (1.17). A bit more of Rama outliers and the most noticeable in the Rotamer outlier score. Is there any reason that could explain such behaviour ? I am using Phenix under MacOS. Xavier Brazzolotto, PhD xavier.brazzolotto(a)chemdef.fr Département de Toxicologie et Risques Chimiques Unité Neurotoxiques Institut de Recherche Biomédicale des Armées 1 Place du Général Valérie André, BP 73 91223 Brétigny sur Orge France Phone +33 (0) 1 78 65 14 00 Alt Phone +33 (0) 4 57 42 87 19 Cell +33 (0) 6 58 36 39 09 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not necessarily complies to the ministry cyber security policy.

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unit cell dimesions
by Thomas, Leonard M. 13 May '20

13 May '20

Hello All, I have run into something that has me a bit puzzled. When finishing up a structure we ended reprocessing the data to get nice statistics for deposition, I don’t want to get into that discussion. Upon reprocessing the unit cell dimensions shifted slightly, 0.05 A or so. The PDB file used had the unit cell from the original solution/refinement while the data set cell dimensions were different. I ran the newly processed reflection data set through the reflection editor in order to transfer the Rfree set. Now the really odd thing is that I ended up reprocessing a couple times and transferring over the Rfree set once more. The cell dimensions on the final reflection file is from not the original reflection file/PDB but one that was used with an intermediate cutoff between the two, it is not the cell dimensions in the input reflection either. Just for completeness the data were processed using XDS at SSRL. My question is where does phenix.refine pick up the unit cell dimensions and were does the reflection file editor pick them up? Best Regards Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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install fail in linux
by 안우찬 12 May '20

12 May '20

Hi, I have a problem with install phenix-1.18.1-3865 in linux. My linux version is NAME="Red Hat Enterprise Linux Atomic Host" VERSION="7.4.0.4". The error massage is ============================================================================= Traceback (most recent call last): File "./bin/install.py", line 244, in <module> installer(sys.argv[1:]).install() File "/home01/x1959a02/phenix/phenix-installer-1.18.1-3865-intel-linux-2.6-x86_64-centos6/li b/libtbx/auto_build/install_distribution.py", line 190, in install self.check_directories() File "/home01/x1959a02/phenix/phenix-installer-1.18.1-3865-intel-linux-2.6-x86_64-centos6/li b/libtbx/auto_build/install_distribution.py", line 268, in check_directories os.makedirs(i) File "/usr/lib64/python2.7/os.py", line 157, in makedirs mkdir(name, mode) ============================================================================= Thanks in advance, Teddy Ahn

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How to compare between electron density maps?
by Murpholino Peligro 12 May '20

12 May '20

I want to compare electron density features of map A from protein A and map B from protein B... Because each map has a different rmsd level... ...what is the best way to compare electron density between maps? Is there a way to normalize maps or something like that? Thanks

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Is there a way to search the phenixbb mailing list archive?
by Murpholino Peligro 11 May '20

11 May '20

With the ccp4bb at https://www.jiscmail.ac.uk/cgi-bin/webadmin I can search for a term in the archive. Is there something similar in the phenixbb? Thanks Or... is there a way to wget all the gz files?

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Online Course on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 11 May '20

11 May '20

ORNL Online Course on Neutron Scattering Applications in Structural Biology (https://conference.sns.gov/event/217/) June 1 - June 5, 2020 2:00 pm - 5:30 pm EST Registration (free) is now open and will close May 17, 2020. This online course is designed for graduate students, post-doctoral researchers and faculty with knowledge of structure and function of biological macromolecules but with limited to no experience with neutron sciences. The course will cover the basics of deuterium labeling, small angle neutron scattering, neutron reflectometry, neutron spectroscopy, neutron imaging and neutron crystallography. Instrumentation, sample preparation, data collection and processing will be introduced for each neutron technique.

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Boost 1.70 update for cctbx
by Billy Poon 09 May '20

09 May '20

Hi everyone, There is currently a pull request for cctbx that will update Boost to 1.70 ( https://github.com/cctbx/cctbx_project/pull/409). The update enables support for Python 3.7 and 3.8. The plan is to merge this next Friday, May 8, at 3 pm Pacific. After merging, developers should delete the build/lib/*boost* files and build/boost directory so that any remnants of the old Boost are removed and then rebuild. Let me know if you have any questions. Thanks! -- 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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Phenix installation
by Sam Tang 06 May '20

06 May '20

Hi I am installing Phenix on a Fedora 30 station. It complains line 15: /usr/bin/python: No such file or directory. I have checked that there is python3.7.3 pre-loaded. So did I miss anything obvious...? Brs Sam

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Ligand refinement - geometry does not fit density
by Schulz, Eike-Christian 04 May '20

04 May '20

Dear all, I am refining a structure with a simple ligand in phenix 1.14. The ligand is present in 2 conformations at approx. equal occupancy. Refinement of the 2 conformations runs smoothly, but 2 problems occur 1. One of the ligand atoms is placed out of the electron density after refinement. The geometry file (via elbow) is present during refinement. The atom is not in an extreme position or clashes with anything else. 2. After refinement the ligand conformation cannot be changed in coot, although I import the cif dictionary. Any advise ? Best, Eike

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Phenix 1.18 RSR runtime
by Hannah Bridges 02 May '20

02 May '20

Dear Phenix developers, We have updated to phenix version 1.18-3845-000 and found that realspace refinement (5 cycles) with minimization global, local grid search and ADP is taking about 36 hours, compared to ~ 1hr in versions 1.17 and 1.16. The slow step is the local grid search which is taking >6 hours each cycle. We are very glad for the option to run the job detached, but I wondered if this sort of timing was expected for this version? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

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off-topic; suggestions for 96head liquid handler
by Georg Mlynek 30 Apr '20

30 Apr '20

Dear Scientific community, we have lend over Viaflow96 liquid handler (used for pipetting 35-50 uL in 96 well crystallization plates) to our Covid -19 Diagnostics Initiative. As we believe that this story will be ongoing for some longer time I am looking for a new 96 head liquid handler. We are happy with the Viaflow and have two heads 10-300 uL; 0.5-12.5 uL. However one tip box (96 tips for the 10-300 uL) is about 4 €. This compares to ~1 € for the refilling racks we use for our single channel pipettes (It is said that boxes have to be more rigid, because of pressure during tip loading). Therefore if you have a 96 head liquid handler for volumes of 20-60 uL where cheap tips can be used (automation not necessary) please write me. Many thanks in advance, best regards, Georg.

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Computational Crystallography Newsletter (CCN) release and submissions
by Nigel Moriarty 28 Apr '20

28 Apr '20

Folks Recent world events have affected many things including the timely release of the CCN. Please consider this the Shelter-In-Place edition. Many of you will be involved in SARS-CoV-2 research and the CCN for July 2020 can be a vehicle for publishing the more community interest details. The deadline for submissions is 1 JUN 2020. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. 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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Open postdoc positions in the Gonen lab
by Johan Hattne 26 Apr '20

26 Apr '20

Dear all; We would like to draw your attention to two HHMI-funded postdoc positions in the laboratory of Tamir Gonen at the University of California, Los Angeles. The first position concerns the biochemistry of membrane proteins, the second is focused on computational methods development. For further information, as well as application instructions, see the links below. Biochemistry https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobin… Programming https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobin… // Best wishes; Johan

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Two conformation of a ligand
by Muhammad Bashir Khan 22 Apr '20

22 Apr '20

Hi All; I have a structure where I believe that the ligand is bind in two conformations. In the Ligand Fit, it places only one even I select conformer 2. My other question is, Is there a way that I can use a reference PDB bound to the ligand in the Ligand Fit to help it placing my ligand. Thanks for your help in advance Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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Problems displaying disulphide links
by Urvashi Sharma 21 Apr '20

21 Apr '20

Dear all, I have a problems displaying disulphide links in PyMoL and CCP4mg for a 2.3 angstrom crystal structure. I have tried both PyMoL and CCP4mg, these programs are not recognizing an important inter-domain disulphide bridge which seems to have no problems in "Coot". While other intra-domain disulphide links are fine. Can anyone suggest how to manually fix it? In addition, I have performed protein-protein docking using this crystal structure and have obtained nice convincing model. However, in this pose, which is being refined and energy minimized, none of the disulphide links are intact! Upon manual examination, I have noticed that the corresponding cysteine are 3.0-4.0 angstrom away. How should I correct this? Looking forward to your suggestions... With thanks and regards, Urvashi ---------------------------------------------------- Dr Urvashi Sharma, DBT-Ramalingaswamy faculty fellow JNU, New Delhi.

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Error log
by Viswanathan Chandrasekaran 16 Apr '20

16 Apr '20

Hi all, Other than resubmitting the job, is there a way to retrieve the contents of the Phenix error dialog box that appears at the end of a failed job? It is not present in the log file. Thanks, Vish

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iNEXT-Discovery: Access to facilities for structural biology research
by a.perrakis＠nki.nl 16 Apr '20

16 Apr '20

Dear all, While being in turbulent times, iNEXT-Discovery, the EC Horizon-2020 project offering access to facilities for structural biology (EM, NMR, X-rays and macromolecular biophysics), has officially started its operations. iNEXT-Discovery encourages applications for structural biology projects for ‘translational research projects’ in the areas of biomedicine, biotechnology, biomaterials and in the food sector, in particular from non-experts and for researchers from academia and industry. We are now happy to announce to the wider research community our new website with details about the project and where applications for access to the participating facilities can be submitted: https://inext-discovery.eu<https://inext-discovery.eu/> Regardless of current corona-measures external researchers are more than welcome to apply for access and we expect reviewing of incoming proposals to proceed as normal. However, please keep in mind that most facilities are currently not operational, and it is uncertain when they will open again to deliver access and to receive visitors. We will not be able to give a detailed overview about the status of all facilities, as the situation is changing almost daily. Having accepted applications in our access pipelines will help both our scheduling and yours. Our facilities can arrange experiments for approved user projects to be executed immediately after local policies allow. Please note that applications addressing SARS-CoV-2 or Covid-19 and mentioning this in the title will be funneled towards rapid review. Operational facilities will prioritize such projects if they can be accommodated. On behalf of the iNEXT-Discovery team, Hans Wienk (Project Manager) - email h.wienk.AT.nki.nl<http://h.wienk.at.nki.nl/> for questions about access Anastassis Perrakis (Coordinator)

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covalently linked ligand
by Muhammad Bashir Khan 15 Apr '20

15 Apr '20

Hi All; I have a protein molecule and a ligand structure. I want to make a covalent bond between the ligand and protein molecule, could somebody explain to me how I can do that using phenix. I used the " *phenix.ligand_linking pdb_file_name" commond* It creates apply_link.def and data_link.cif I did refine the structure again giving the above file as well but did not see any covalent bond created between the protein and ligand. Thanks for your help Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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helix/sheet outliers
by Casper Larsen 14 Apr '20

14 Apr '20

Hi.. I am doing real space refinement on a protein model build from a cryo-em map. I run the refinement with Amber gradients turned on and with secondary structure restraints (otherwise, more or less default settings). I have some issues with helix and sheet outliers. Every time I run the refinement (after making sure that the bond distance in the helices are within the 3.5 Å) I get a lot of bad annotation remarks, but with outliers just above 3.5 Å (see .log below): ... removed outlier: 3.576A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.681A pdb=" N PHE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.737A pdb=" N MET A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) ... Is this something that I just need to fix in several rounds of refinement or is there an explanation? Amber gradients maybe? In addition, I have some bad sheet annotations such as: ... removed outlier: 6.987A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) ... When I look at the model, the residues are definitely a part of the sheet - the long distance between the N-O atoms is due to the O being "flipped" (hope it makes sense). Is this because of wrong annotation? Best Casper

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Advanced Light Source open for COVID-19 related research
by Paul Adams 14 Apr '20

14 Apr '20

Dear Colleagues, A quick note to alert researchers to the status of the Advanced Light Source in Berkeley (https://als.lbl.gov): The ALS is now operating in a limited capacity supporting COVID-19 related research. A number of MX beamlines from the ALS-ENABLE program are now taking proposals from the general user community working on COVID-19 via the ALS RAPIDD program (https://als.lbl.gov/rapidd/); choose ALS-ENABLE as the beamline and your proposal will receive prompt review with fast turnaround for beamtime. We are evaluating the possibility of expanding access to include to other techniques such as soft X-ray tomography, and BioSAXS in the near future. Please feel free to contact me with any questions. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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app which can calculate the number of reflections for a given unit cell, spacegroup, resolution?
by Georg Mlynek 13 Apr '20

13 Apr '20

Dear Scientific community, I am looking for an app which can calculate the number of reflections for a given unit cell, spacegroup, resolution. Preferred would be a graphical output too. The program XRayView http://www.phillipslab.org/downloads comes very close what I imagine but it is not possible to select a spacegroup. It would like to use it for teaching parts of practical part during lockdown. Many thanks, br Georg.

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