- phenixbb - phenix-online.org

Lectureship Positions University of Kent
by Gary Thompson 07 Aug '19

07 Aug '19

We have two Jobs advertised at the University of Kent that may be of interest to structural biologists with expertise in macro molecular crystallography. https://jobs.kent.ac.uk/Vacancy.aspx?ref=STM-032-19 The School of Biosciences has a long and continuing interest in structural biology with several groups exploiting NMR and Macromolecular Crystallography to study a wide range of problems. These include infection and drug resistance, cancer and age-related diseases, cellular architecture and dynamics and reproduction, evolution and genomics and industrial biotechnology. The School of Biosciences consistently has time as a BAG at Diamond and has recently invested in a new Mosquito LCP System with humidity control for crystallisation drop set up. Other facilities available for structural biologists include a well equipped Biomolecular Science Facility (electrospray and MALDI-TOF mass spectrometers, peptide synthesisers, CD etc) an in house X-Ray source in the School of Physical Sciences (Rigaku Oxford Diffraction Supernova) and a dedicated Biological NMR Facility with BAG access at the UK national NMR facilities at the Crick and Birmingham. Applications close 23.59 hours BST 19th August. See Job Description for further details. regards gary ------------------------------------------- Dr Gary S Thompson School of Biosciences, University of Kent, Canterbury, Kent, England, CT2 7NZ tel: 01227 82 7117 e-mail: g.s.thompson(a)kent.ac.uk<mailto:[email protected]> orchid: orcid.org/0000-0001-9399-7636<http://orcid.org/0000-0001-9399-7636> -------------------------------------------

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Phenix downloads are now available
by Billy Poon 06 Aug '19

06 Aug '19

Hi everyone, We fixed the issue with our server, so downloads are now available. We apologize for the inconvenience and please let us know if you encounter any issues. 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 downloads are currently unavailable
by Billy Poon 06 Aug '19

06 Aug '19

Hi everyone, There is currently an issue with the server hosting the Phenix downloads. We are looking into it and we will post and update when the issue is resolved. -- 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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Ligand build in coot
by Pham, Hang 01 Aug '19

01 Aug '19

Hello, I have an alpha-lactose as ligand in my model. It is possible that the glucose ring of alpha-lactose is opened since I do not see the whole density of ring and there are an extend density after C2’ of the glucose molecule. Does anyone know how to cleave the covalent between O’ and C1’ to form linear glucose in coot or should I build a new ligand from beginning (beta-galactose cyclic forming beta-1-4 glycosidic linkage with a linear glucose) in coot ? Thank you in advance Hang Pham ------------------------------------------------------ Hang Pham, Ph.D Student, The Doucet Lab Centre Armand-Frappier Santé Biotechnologie Institut National de la Recherche Scientifique (INRS) Université du Québec Réseau International des Instituts Pasteur 531 Boulevard des Prairies Laval (Québec) H7V 1B7 CANADA Téléphone : (450) 687-5010, poste 4210 Site web: http://www.profs.inrs.ca/ndoucet/

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General interest
by John R Helliwell 01 Aug '19

01 Aug '19

Dear Colleagues, The details, including all abstracts, for the IUCr Satellite at ECM32 Vienna on Data Science Skills in Publishing for Editors, Authors and Referees can be found here:- https://forums.iucr.org/viewtopic.php?f=39&t=419 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

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Phenix, MolProbity, and Amber
by Eric Williams 30 Jul '19

30 Jul '19

Greetings, all I'm trying to run the MolProbity programs (reduce, ramalyze, etc) in Phenix 1.16-3649, and I get the following warning: "Could not import the compiled Python-sander interface. Make sure you have the Python development libraries installed and that you have sourced amber.sh or amber.csh" I do not recall seeing that in earlier versions. Do I need to worry about it? If so, how do I fix it? Thanks. :) Eric

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General interest
by John R Helliwell 30 Jul '19

30 Jul '19

Dear Colleagues, For your general interest, you can find the lecture slides that I presented at ACA 2019 in the Transactions Symposium on Data via the weblink here:- https://forums.iucr.org/viewtopic.php?f=39&t=421 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of IUCr CommDat

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ISOLDE dev builds now available
by Tristan Croll 30 Jul '19

30 Jul '19

Hi all, Since the release of ISOLDE 1.0b3 I've begun releasing regular (weekly~fortnightly) development builds of ISOLDE. These are built against the ChimeraX daily build at the time of release - if you download a ChimeraX-daily build and install ISOLDE in the usual way via Tools/More Tools... this is what you'll get. In case you're worried, the dev and official 1.0b3 builds install into different directories, so it's quite straightforward to have both versions running independently on the same machine. The dev builds are *not* compatible with the ChimeraX 0.9 stable release. Some important changes since 1.0b3/ChimeraX 0.9: - the ChimeraX team have fixed some bugs affecting PDB and mmCIF I/O (primarily involving the handling of "imperfect" files) - fixed a bug causing the simulation to crash if the minimiser didn't converge in the first round - added status messages during simulation startup, and clear indications of when a simulation is running/paused - improved simulation startup time, and handling of custom ligands (preparing ligand definition files is a work in progress and will currently need you to do some work outside ISOLDE - feel free to contact me if you have an urgent case) Best regards, Tristan

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modify.remove option in phenix.refine
by wtempel 29 Jul '19

29 Jul '19

Hi, for calculation of an omit map, with the atoms in question fully removed from the model, I experimented with the modify_start_model.modify.remove option and got: ====================== Modifying start model if requested ===================== Size before: 505 size after: 491 Traceback (most recent call last): File "/home/user1/phenix-1.16-3549/build/../modules/phenix/phenix/command_line/refine.py", line 11, in command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/user1/phenix-1.16-3549/modules/phenix/phenix/refinement/command_line.py", line 106, in run log=log) File "/home/user1/phenix-1.16-3549/modules/phenix/phenix/refinement/driver.py", line 271, in __init__ self.model.set_xray_structure(modify_model_obj.xray_structure) File "/home/user1/phenix-1.16-3549/modules/cctbx_project/mmtbx/model/model.py", line 693, in set_xray_structure self.set_sites_cart_from_xrs() File "/home/user1/phenix-1.16-3549/modules/cctbx_project/mmtbx/model/model.py", line 1722, in set_sites_cart_from_xrs self._pdb_hierarchy.adopt_xray_structure(self._xray_structure) File "/home/user1/phenix-1.16-3549/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 688, in adopt_xray_structure raise RuntimeError("Incompatible size of hierarchy and scatterers array.") RuntimeError: Incompatible size of hierarchy and scatterers array. I verified that my intended selection indeed comprises 14 atoms. Has anyone used the remove option inside phenix.refine successfully. Thanks. Wolfram Tempel

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cbf to sfrm
by Tim Gruene 28 Jul '19

28 Jul '19

Dear all, recently the conversion from CBF to SFRM frame format with APEX was discussed on the Bruker mailing list ("Synchrotron data with Bruker Software"), including a potential bug that parameters in the frames other than the first frame are not set correctly. The workaround to re-convert from SFRM to SFRM a second time did not help in my case. I therefore updated my program sfrmtools, available at https:// homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/ With the option '-u',you can provide the first frame of the run, and via '-p' a parameter file that contains the critical parameters (see documentation at above URL) to update the header for all frames in this run. In case you have twinned data and want to benefit from SAINT, this should be possible with this feature. Both 64bit Linux binary and the source code are available. The program has no dependencies and should compile under any platform. I did not debug this new feature very thoroughly, but it worked for me so far. Any bug reports are welcome to this address tim.gruene(a)univie.ac.at I hope this is helpful for one or two users. I acknowledge the thorough documentation of XDS, of SAINT, and of the SFRM header format. Kind regards, Tim cc Bruker mailing list, CCP4BB, phenixBB -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A

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Unwanted LINK records
by Luca Pellegrini 27 Jul '19

27 Jul '19

Hello, Phenix.real_space_refine generates a few spurious covalent bonds between protein and ligand in my structure, which distort the local structure, and then adds the corresponding LINK records in the output file. Is there a way to avoid this? I am aware of the anti-link option previously mentioned in the phenixbb: http://www.phenix-online.org/pipermail/phenixbb/2018-January/023677.html, but I was wondering if there was another way of preventing this from happening. I am using Phenix 1.15.2-3472. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Symmetry of map vs Symmetry of model
by pramod kumar 27 Jul '19

27 Jul '19

Dear all, I have a query related to symmetry imposition and corresponding tweaking of model. If symmetry (say, C4) was imposed during the reconstruction of a 3D volume, does symmetry also need to be imposed when building the atomic model (say, in Phenix)? Or could this constrain be relaxed? Do we need to tweak the model in Coot for other chains or since it is build on symmetrical partners therefore should only be made in one chain and copied for all without any fitting? Pramod Jaykar, Ph.D.

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Re: [phenixbb] Unwanted LINK records
by Dale Kreitler 26 Jul '19

26 Jul '19

Hi Luca, Try running with the parameter: refinement.pdb_interpretation.automatic_linking.link_ligands=False Check if automatic linking is enabled with the All parameters button in the GUI. Looks like the default might be True? -D On Fri, Jul 26, 2019 at 11:21 AM Luca Pellegrini <lp212(a)cam.ac.uk> wrote: > Hello, > > Phenix.real_space_refine generates a few spurious covalent bonds between > protein and ligand in my structure, which distort the local structure, and > then adds the corresponding LINK records in the output file. Is there a way > to avoid this? > > I am aware of the anti-link option previously mentioned in the phenixbb: > http://www.phenix-online.org/pipermail/phenixbb/2018-January/023677.html, > but I was wondering if there was another way of preventing this from > happening. I am using Phenix 1.15.2-3472. > > Best wishes, > Luca > > Luca Pellegrini, PhD > Department of Biochemistry > University of Cambridge > Cambridge CB2 1GA > United Kingdom > > lp212(a)cam.ac.uk > tel.: 0044 1223 760469 > https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group > @PellegriniLab > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > -- Dale Kreitler Graduate Research Assistant Gellman Lab Department of Chemistry University of Wisconsin-Madison

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Symmetry of map Vs Symmetry of model
by pramod kumar 26 Jul '19

26 Jul '19

Dear all, I have a query related to symmetry imposition and corresponding tweaking of model. If symmetry (say, C4) was imposed during the reconstruction of a 3D volume, does symmetry also need to be imposed when building the atomic model (say, in Phenix)? Or could this constrain be relaxed? Do we need to tweak the model in Coot for other chains or since it is build on symmetrical partners therefore should only be made in one chain and copied for all without any fitting? Pramod Jaykar, Ph.D.

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CryoEM specialist positions open at CSIR-CCMB, India
by Rukmini Raju 23 Jul '19

23 Jul '19

Dear All, This is to bring to your kind attention two vacancies for Structural Biologists with CryoEM expertise at the CCMB, Hyderabad, India. CSIR-Centre for Cellular and Molecular Biology, Hyderabad (CSIR-CCMB) is a Premier Research Laboratory under the Council of Scientific & Industrial Research (CSIR), involved in multidisciplinary R&D programmes of both basic and applied nature across scientific disciplines of biological sciences. The link for the application is given below: http://www.ccmb.res.in/index.php?view=notifications&mid=0&id=71&nid=268 Best regards, Sankar -- ****************************************************************************** Dr. Rajan Sankaranarayanan Chief Scientist, Structural Biology Laboratory CSIR-Centre for Cellular and Molecular Biology (CCMB) Uppal Road Hyderabad - 500 007 India. Ph: +91-(0)40 2719 2832 to 2835 (Lab) +91-(0)40 2719 2500 (CCMB Reception) Fax: +91-(0)40 2716 0252, 2716 0591 e-mail: sankar(a)ccmb.res.in sankarfr(a)yahoo.com Web: http://e-portal.ccmb.res.in/e-space/sankar/index.html ******************************************************************************** -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ R. Rukmini Principal Technical Officer Structural Biology, R-100, R&D Building CSIR-Centre for Cellular and Molecular Biology Uppal Road, Hyderabad - 500 007 India Phone# +91-40-27192953(callto:+91-40-27192953) (R-100) +91-40-27192835(callto:+91-40-27192835) (Lab, Main Building) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Real space refinment keeps messing up my taxol conformation
by Ahmad Khalifa 20 Jul '19

20 Jul '19

I used elbow to generate restraints for taxol using chemical componenet and sdf file. I posted before to the list and Oleg was kind enough to provide restraints generated by readyset. No matter what restraints I use, the taxol is messed up! The other thing is, the refinement keeps breaking the peptide bond at a specific location! I would like to send some files to someone privately to investigate! Please let me know. Regards.

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phenix.pdbtools
by Raja Dey 18 Jul '19

18 Jul '19

Dear Members, I like to regularize the geometry of selected residues' side chains using phenix.pdbtools? I couldn't find the syntax. I used the following command line syntax, but didn't work. Can someone help correcting this command? phenix.pdbtools myprotein.pdb geometry-regularization=true selection="((chain A and ((resseq 236:237 not backbone) or (resseq 240:241 not backbone) or (resseq 244 not backbone) or (resseq 254 not backbone) or (resseq 258 not backbone) or (resseq 261:262 not backbone) or (resseq 412:413 not backbone) or (resseq 416:417 not backbone) or (resseq 419 not backbone))) or (chain X and ((resseq 104 not backbone) or (resseq 107:108 not backbone) or (resseq 111 not backbone) or (resseq 113 not backbone)))) Best regards, Raja

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Understanding Biology through Structure, March 16-20, 2020 in Santa Fe, NM
by Tom Terwilliger 18 Jul '19

18 Jul '19

Hi Structural biologists, particularly students and postdocs! I hope that you can come to our second "Understanding Biology through Structure” conference, to be held in Santa Fe, NM March 16-20, 2020. The purpose of the conference is to provide a forum for students and postdocs to meet established researchers as well as some rising stars, and to see and discuss presentations on the latest methods and results. The last conference was a huge success (see https://bit.ly/2Gfkm4t and https://bit.ly/2Gg39rm) and this one is looking great (see https://cvent.me/4kq9P) We have a super group of speakers (keynote speakers are Ilme Schlichting, David Stuart, Erica Ollmann Saphire, Robert Stroud, Suzanne Scarlata, David Eisenberg, Wayne Hendrickson, Yvonne Jones, Eva Nogales, and Tom Blundell), and all the talks will be followed by 10-15 minutes of discussion with participation by students and postdocs especially encouraged. There are a number of fellowships covering hotel and registration available for students and postdocs. Successful applicants will be notified on a rolling basis about a month after they register for the conference. After the main conference there will be an optional Phenix workshop with lectures and hands-on sessions on using Phenix for crystallography and cryo-EM. You can register now at https://cvent.me/4kq9P ! Best regards, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Broken Phenix Coot integration after upgrade to v 1.16
by Ahmad Khalifa 17 Jul '19

17 Jul '19

Hello, After the update, when I open coot from validation with Phenix integration, and navigate to different atoms, clashes, etc, I get moved to an empty space outside of my map and model. What's going wrong here? Regards.

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Phenix real space refine problems
by Gyles Cozier 16 Jul '19

16 Jul '19

Good afternoon, I have been having issues with the last 3 versions of Phenix (1.14, 1.15 and 1.16) when the XYZ(real-space) option is selected, version 1.13 was the last one that doesn't have this problem for me. This seems to place too much weight on correcting rotamer 'outliers' at the expense of fitting to the density. The proteins that I work on have always had some residues that consistently are identified as rotamer outliers, but these latest versions 'correct' just about all of them (typically from 1% down to 0.1%). The resulting structures show clear movement of the sidechains out of what should be their density. Image 1 (after using 1.13) and 2 (after using 1.14, 1.15 or 1.16) show a really bad example where the Arg sidechain even gets broken apart to be moved into the stronger density of a neighbouring symmetry Gln. Image 3 (after using 1.13) and 4 (after using 1.14, 1.15 or 1.16) is a more subtle example, but although the residue is no longer a rotamer outlier after refinement using 1.16, it clearly does not fit the density as well as after using 1.13. These subtle changes are particularly worrying, as they could easily be missed when checking the structure after refinement. Other members of the group have also noticed this problem for different proteins. So currently I have a choice of either using version 1.13 (which with Onedep no longer accepting pdb files makes things a bit inconvenient as is nice to use the latest version for getting the mmcif and validation), or to use 1.16, but switch off the XYZ(real-space). Has anyone else noticed this happening? Found a solution to the problem? Thank you for any suggestions, Gyles Cozier.

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upgrading phenix version on linux
by Ahmad Khalifa 15 Jul '19

15 Jul '19

Hello, How should I upgrade my Phenix installation? Remove the old one first, or install to a different directory keeping both? Does the new installation take care of it already?! Regards.

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Berkeley Web Services Downtime
by Paul Adams 13 Jul '19

13 Jul '19

Dear Colleagues, as a result of electrical work at LBNL the following servers will be unavailable over the weekend: - 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 some time on Monday July 15th. 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. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab (https://als.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) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Opportunity in the Gonen lab
by Johan Hattne 13 Jul '19

13 Jul '19

Dear all; There is an exciting opportunity for a research technician to join the Gonen lab at UCLA, supporting ongoing projects in membrane biophysics and biochemistry. This role will perform research using biochemical and molecular biology techniques. The Gonen Lab at the University of California works toward understanding how membrane proteins help cells maintain homeostasis. To that end we study channels, transporters, and receptors structurally and functionally. Complete job posting and application instructions can be found at: https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobin… // Best wishes; Johan Research Specialist @ Gonen Lab ____________________________________________________ UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095

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High B factors
by ssolmaz 12 Jul '19

12 Jul '19

Dear Kay, Thank you, this is helpful. Yes, the data were collected at the synchrotron with a Dectris Pilatus 6MF detector. CC1/2 at the highest resolution shell (2.55A - 2.5A) is 0.481 and I/sigma(I) is 1.2. The multiplicity is 9.7. Best, Sozanne. Sozanne Solmaz, Ph. D. Assistant Professor of Biological Chemistry Department of Chemistry, State University of New York at Binghamton PO Box 6000, Binghamton, NY 13902 Office: Smart Energy Building Room SN1045 25 Murray Hill Road, Vestal, NY, 13850 http://chemiris.chem.binghamton.edu/SOLMAZ/solmaz.html

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Re: [phenixbb] High B factors
by Kay Diederichs 12 Jul '19

12 Jul '19

Dear Sozanne, I expect these data were collected at a synchrotron, and they are quite weak at 2.5A? (would be good to know CC1/2 in the high-resolution shell) If so, what you see is normal, and there's most likely nothing wrong with your data or model. I've seen Wilson and average B-factors higher than the ones you cite, for perfectly correct models and well-measured data. It is just a fact that your protein's atoms vibrate in the lattice, and the B factors are a way to measure how much. There is a mathematical relation between B-factors and strength of diffraction at high resolution; the higher the former, the lower the latter. best, Kay On 7/11/19 6:49 PM, phenixbb-request(a)phenix-online.org wrote: > Date: Thu, 11 Jul 2019 11:50:52 -0400 > From: ssolmaz <ssolmaz(a)binghamton.edu> > To: phenixbb(a)phenix-online.org > Subject: [phenixbb] High B factors > Message-ID: > <CAHYfRfKKMViLmaEuVr0aANGu6iaW6ofMAWSKHZ5JuCnOusFQ4w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > We recently determined a protein structure by molecular replacement and the > statistics are looking good, however, the average B-factor is unusually > high, and the Wilson B-factor is high too. A quick research on the subject > suggested that high B-factors are acceptable as long as one has excluded > and double-checked for other crystallographic problems. Which problems > should I check for and what is your opinion on the high B-factor? Is there > anything that could be done to lower it? > > Resolution: 2.5 A > Space group P3121, 60.0 60.0 142.6 90 90 120 > R work 24.6% > R free 26.4% > Wilson B-factor 73.2 > Average B-factor 99.5 > > Thank you for your advice, > Best, Sozanne. > > Sozanne Solmaz, Ph. D. > Assistant Professor of Biological Chemistry > Department of Chemistry, State University of New York at Binghamton > PO Box 6000, Binghamton, NY 13902 > Office: Smart Energy Building Room SN1045 > 25 Murray Hill Road, Vestal, NY, 13850 > http://chemiris.chem.binghamton.edu/SOLMAZ/solmaz.html -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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Comprehensive validation fatal problems interpreting model
by Ahmad Khalifa 11 Jul '19

11 Jul '19

Hello, I have a fatal error with my model regarding a number of atoms with unknown nonbonded energy type symbol! I attached a screenshot of the error and my pdb, can you please help me debug the problem? Best regards.

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Phenix website, servers and bulletin board
by Nigel Moriarty 11 Jul '19

11 Jul '19

Folks Due to the rerouting of 12kV underground transmission lines near our building, there will interruptions to Phenix computer services starting 12 July for about a week. The plan calls for only short outages but please be prepared for anything. 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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High B factors
by ssolmaz 11 Jul '19

11 Jul '19

Dear all, We recently determined a protein structure by molecular replacement and the statistics are looking good, however, the average B-factor is unusually high, and the Wilson B-factor is high too. A quick research on the subject suggested that high B-factors are acceptable as long as one has excluded and double-checked for other crystallographic problems. Which problems should I check for and what is your opinion on the high B-factor? Is there anything that could be done to lower it? Resolution: 2.5 A Space group P3121, 60.0 60.0 142.6 90 90 120 R work 24.6% R free 26.4% Wilson B-factor 73.2 Average B-factor 99.5 Thank you for your advice, Best, Sozanne. Sozanne Solmaz, Ph. D. Assistant Professor of Biological Chemistry Department of Chemistry, State University of New York at Binghamton PO Box 6000, Binghamton, NY 13902 Office: Smart Energy Building Room SN1045 25 Murray Hill Road, Vestal, NY, 13850 http://chemiris.chem.binghamton.edu/SOLMAZ/solmaz.html

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exclude atoms/regions in real space refinement
by Filip Van Petegem 05 Jul '19

05 Jul '19

Dear Phenix users, I want to exclude particular regions of a protein model, docked into a cryo-EM map, from real-space refinement. I know this is possible for refinement in reciprocal space, but is this possible for refining a cryo-EM structure against a map? E.g. I want to totally exclude a region with known crystal structure, placed in an area of poor local resolution, from any form of refinement, but want to apply all other options (morphing, simulated annealing, adp, Global minimization) to the remainder of the structure. (I didn't see this option in https://www.phenix-online.org/documentation/reference/real_space_refine.html ) best regards, Filip -- Filip Van Petegem, PhD Professor, Dept. of Biochemistry and Molecular Biology The University of British Columbia 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpetegem(a)gmail.com http://crg.ubc.ca/VanPetegem/

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AUC2019. Registrations still open. Graduate and Postdoctoral scholarship awards available.
by Renwick Dobson 04 Jul '19

04 Jul '19

Dear Structural biology community, AUC2019<https://auc2019.uleth.ca/>, the 24th AUC Workshop and Symposium, will be held at the University of Canterbury, Christchurch (New Zealand) from 24-29 August 2019. 1) Registrations are now open and details can be found at this website: https://auc2019.uleth.ca/. Early Bird Registrations have been extended to the 15th July. 2) Beckman Coulter Life Sciences is generously offering one scholarship to a Graduate student and one to a Postdoctoral fellow to attend AUC2019 in Christchurch, New Zealand. Awardees will have their transportation (including airfare) and registration to the symposium and workshops covered (to a value of $1500USD). In addition, awardees will give a short talk in the symposium on their research. If you are interested, please submit the following to Ren Dobson (renwick.dobson(a)canterbury.ac.nz<mailto:[email protected]>) by the 18th July: i) a 400 word summary on how AUC has been used in your research, or alternatively, how you intend to use AUC during your research. (in pdf format) ii) A CV (in pdf format) iii) a scientific abstract for the talk. A template for the abstract is here: https://www.dropbox.com/s/sccrqoyp9wo7alm/NZ.AUC2019_AUC_SampleAbstract_for…. (submit in pdf format) Note, deadline for the Beckman Coulter Scholarships is the 18th July. The winners will be announced by the 31st July. 3) As the scientific program<https://auc2019.uleth.ca/symposium.php> for AUC2019 emerges, events will be uploaded to the website. We strongly encourage you to submit abstracts for talks and posters<https://auc2019.uleth.ca/abstracts.php>. 4) The format of the event is a 2-3 day workshop<https://auc2019.uleth.ca/workshops.php> offering parallel, hands-on training in experimental design and the latest AUC data analysis software from the world experts in this area followed by a 2 day research symposium on AUC and complementary approaches: methodological development, combination with orthogonal techniques (SAXS, SANS, SPR, MST, SEC-MALLS etc), application in biosciences and material sciences. 5) The meeting is also timed such that delegates can also attend the Biomolecular interactions and Engineering Symposium<https://www.queenstownresearchweek.org/bio-interactions/>, which is part of the Queenstown Molecular Biology Conference (this is in Queenstown, NZ), although note that this is a separate conference. 6) Lastly, The European Biophysics Journal has kindly agreed to run a special issue to celebrate the research presented at AUC2019. Therefore, we invite those who wish to extend their talks to a journal publication to consider contributing original research articles to this issue. Please indicate your interest for inclusion in this volume below. Deadline for registration of a contribution is August 30 2019. We look forward to welcoming you to Christchurch, New Zealand next Spring(-ish)! Ren Dobson, Chair AUC2019 On behalf of the AUC2019 Scientific Organising Committee ---- Prof. Ren Dobson Co-Director, Biomolecular Interaction Centre (BIC) http://www.bic.canterbury.ac.nz/ School of Biological Sciences | Te Kura Pūtaiao Koiora University of Canterbury | Te Whare Wānanga o Waitaha Private Bag 4800 Christchurch | Ōtautahi New Zealand | Aotearoa E: renwick.dobson(a)canterbury.ac.nz<mailto:[email protected]> T: ++64 (03) 369-5145 x 95145 F: ++64 (03) 364-2590 W: http://dobsonlab.org/

1 0

intensity merging statistics for wwpdb deposition
by wtempel 03 Jul '19

03 Jul '19

Dear PHENIX users, how does one add merging statistics to PHENIX mmcif coordinates for deposition, assuming availability of AIMLESS logs and pre-merge intensities? Is this functionality implemented in PHENIX or CCTBX? Thanks. Wolfram Tempel

1 0

r_work and r_free from an .mtz file containing Fobs and Fcalc
by Andre LB Ambrosio 01 Jul '19

01 Jul '19

Dear colleagues, Can Phenix calculate r_work and r_free from a .mtz file containing FP and FC_ALL (from PDB_REDO), without inputing the matching .pdb file? Many thanks in advance, -- Andre LB Ambrosio

2 5

6th International Symposium on Diffraction Structural Biology: First Announcement
by Leighton Coates 01 Jul '19

01 Jul '19

Dear Colleague You are invited to the 6th International Symposium on Diffraction Structural Biology which will take place at the University of Osaka in Japan. Start Date: 17th Oct 2019 End Date: 20th Oct 2019 URL: https://isdsb2019.symposium-hp.jp/ The 6th International Symposium on Diffraction Structural Biology (ISDSB2019) is an international symposium organized by the Japan Society for the Promotion of Science, University-Industry Research Cooperative Research Committee, 169th Committee on Structural Biology using Diffraction Techniques. This symposium is positioned as an interface between academic researchers and industry researchers, as well as an interface between diffraction techniques and other related techniques in the field of structural biology. Symposium topics will include Macromolecular crystallography, CryoEM, software and databases, and drug discovery, registration and abstract submission for the symposium is now open and costs 25,000 Japanese yen for academics. A list of confirmed speakers for the symposium is currently being finalized; this will be posted on the symposium website within the next few days. Contact: Atsushi Nakagawa (Osaka University) Email: isdsb2019(a)gmail.com URL: https://isdsb2019.symposium-hp.jp/

1 0

Mandatory PDBx/mmCIF format for crystallographic PDB depositions
by John Berrisford 01 Jul '19

01 Jul '19

>From today, July 1st 2019, submission of PDBx/mmCIF format files for crystallographic depositions to the PDB is mandatory. Refmac, Phenix.refine, and Buster programs can now output PDBx/mmCIF formatted files. For users of other structure determination/refinement software packages, the wwPDB provides stand-alone and web-based tools to convert legacy PDB format files into PDBx/mmCIF format: pdb_extract <http://pdb-extract.wwpdb.org/> and MAXIT <http://sw-tools.rcsb.org/apps/MAXIT/index.html> . More information on outputting and preparing PDBx/mmCIF format files for deposition can be found on the wwPDB website <https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files> . For more information, view the full news release at the wwPDB website <https://www.wwpdb.org/news/news?year=2019#5d17c1ceea7d0653b99c87e2> or contact the wwPDB on deposit-help(a)mail.wwpdb.org <mailto:[email protected]> . Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/proteindatabank> http://www.facebook.com/proteindatabank <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

1 0

PEG as a polymer
by Felix Cat 30 Jun '19

30 Jun '19

Hi all, I'm working on a structure where I see extensive interaction of the protein with PEG (polyethylene glycol). The largest PEGs I can find in structures in the PDB with a quick search are around 12 EDO subunits long, and they're called "dodecaethanediol" or the like. I am seeing at least 20. Currently, I've built the PEG as a giant, single ligand, and generated a viable cif file for it using eLBOW with a SMILES string (very simple for PEG, you can imagine). I'm wondering if I might rather be able to handle it as a polymer of EDO subunits. I started to dig into that but got lost pretty quickly. I can't figure out how to create an automatically link-able EDO molecule, all with proper geometry, and I don't want to have to tell phenix.refine about 19+ custom linkages every time. (I've had to do that with N-linked acetylglucosamine moieties in the past.) Nate NUNC

1 0

Real space refinement with helical symmetry
by Yangqi Gu 29 Jun '19

29 Jun '19

Hi all, I am trying to do a real space refinement with phenix and my map is a filament and I have monomer model and I would like to refine against my filament map. I am wondering how to impose the helical symmetry in this case? (I have a pseudo filament model by copying multiple subunits and aligned in Chimera using "fit in map"). Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

2 1

CaBLAM fixing and interpretation in comprehensive validation for cryo-EM
by Ahmad Khalifa 28 Jun '19

28 Jun '19

Hello, I would appreciate some insights on how to interpret the validation results under the CaBLAM tab and how to use it to fix my structure in Coot? What are the CaBLAM score, the Ca geometry score, the helix score and the 3-10 score? How to use the information under the secondary structure tab? In my protein for example, I see a lot of "try beta sheets", should I try to refine that segment using beta sheets restraints? Best regards.

3 2

(no subject)
by Pu Qian 28 Jun '19

28 Jun '19

Hi All I have a problem to do refinement for one of our cryo-em model caused by ligand of spirilloxanthin (wwPDB code CRT). I'm using phenix cryo-EM real-space refinement for one of my cryo-em models which contains a ligand called spirilloxanthin, a very common carotenoid molecule found in nature. Its code is CRT which can be found in wwPDB ligand dictionary and in COOT. However, when I run real-space refinement, I got a error message caused by this ligand "Fatal problem interpreting model file: Number of atoms with unknot non bonded type symbols: xxx please edit the model file to resolve the problem and /or supply a cis file with matching restrain definitions, along with apply_cif_modification and apply-cis-link parameter definitions if necessary". I checked my pdb file. All atom names and order are exactly same as that in wwPDB. I also try to insert it into map using COOT monomer find method. It does not work as well. It seems to me that Phenix can not recognise this ligand, CRT spirilloxanthin. Does anyone have an idea of how to deal with this issue. Or is it OK if I add CRT.cif into upload window of Phenix for refinement? Any suggestion is greatly appreciated. The version of Phenix I am using is Mac version recently downloaded from Phenix website. Best regards

2 1

Position Opening: Synchrotron Macromolecular Crystallographer @ IMCA-CAT
by Lisa J. Keefe 28 Jun '19

28 Jun '19

Dear Colleagues, POSITION: Synchrotron Macromolecular Crystallographer LOCATION: IMCA-CAT at the Advanced Photon Source (near Chicago, IL) The Industrial Macromolecular Crystallography Association - Collaborative Access Team (IMCA-CAT) and the Hauptman-Woodward Medical Research Institute (HWI) seek an inventive macromolecular crystallographer to join the IMCA-CAT team in accelerating pharmaceutical drug discovery through synchrotron-based structural biology research. As an employee of HWI, you will be based at the center of the team’s operations at the Advanced Photon Source (APS), Argonne National Laboratory, near Chicago, IL. This is an ideal position for a motivated scientist who is passionate about delivering strategic value, developing new technologies, and working in a high- powered, collaborative environment. DESCRIPTION: This is an exciting time to join IMCA-CAT. Underway this summer is the first of a two-phase upgrade that will significantly increase throughput and establish a strong foundation upon which to build capacity. The second phase upgrade, currently in design, will profoundly increase capacity and dramatically expand capability for challenging research projects. The successful candidate will be an integral part of these upgrade activities while maintaining flow of diffraction data for pharmaceutical research projects. The candidate will work closely with IMCA-CAT colleagues in an inclusive and respectful environment, and is expected to take initiative and contribute to the team effort. On any given day, you will do one or all of these things: • Contribute to drug discovery research efforts using a growing portfolio of synchrotron sources. • Enhance the structural biology programs for pharmaceutical structure-based drug design. • Provide experiment support for scientists from the structural biology community who conduct research using the IMCA-CAT synchrotron beamlines. • Ensure beamline instrumentation is operational and produces data of the highest quality. • Expand the experiment envelope of the beamline. • Establish efficient protocols for accelerating data acquisition while enhancing data security. • Develop automated methods for acquiring quality data from challenging samples. • Participate in highly collaborative working groups. • Engage in the technical development of new strategies for ultra-high throughput. • Collaborate with staff on strategically-aligned research and development projects. • Communicate with researchers and present at meetings. • Conduct independent and/or collaborative research. DESIRED SKILLS and EXPERIENCE: • PhD in a relevant field. • Expertise in macromolecular crystallography. • Outstanding experimental skills. • Considerable mechanical skills. • Highly collaborative and team-oriented approach to conducting work and solving problems. • Excellent written and oral communication skills. • Deeply proactive approach to meeting and exceeding goals. • Ability to meet requirements for site access to Argonne National Laboratory. TO APPLY: Send an introductory email, cv, and contact information for three references to Lisa Keefe, IMCA-CAT Director and HWI Vice President of Advancing Therapeutics, at keefe(a)imca-cat.org. LEARN MORE: Visit our websites to learn more about IMCA-CAT (www.imca-cat.org) and HWI (www.hwi.buffalo.edu). HWI is an equal opportunity employer. Lisa J Keefe, PhD Director IMCA-CAT <http://www.imca-cat.org/> Industrial Macromolecular Crystallography Association - Collaborative Access Team 630.252.0544 • Sector 17 @ Advanced Photon Source, Argonne National Laboratory Vice President for Advancing Therapeutics Hauptman-Woodward Medical Research Institute <http://hwi.buffalo.edu/> Past-President American Crystallographic Association <http://www.amercrystalassn.org/> .

1 0

Copying mtz file
by Cygler, Miroslaw 25 Jun '19

25 Jun '19

Hi Phenixers, I have copied mtz file to a new file with a lower resolution limit using the "Reflection file editor” tool. I copied all arrays to the output file. When I attempted to continue refinement with the new mtz file, a message appears saying that there are no R-free flags in the mtz file. Yet, the new file contains the R-free-flags column but the values are inverted, 1 is changed to 0 and 0 is changed to 1. In the output option dialog the box “Preserve original flag values” was checked. How to fix this? Thanks, Mirek

4 3

Why the correlation coefficient of the electron density with the model is never 1?
by Murpholino Peligro 24 Jun '19

24 Jun '19

The links below show a plot of the results of phenix.real_space_correlation* for a nice lisozyme crystal and also the coot view. https://drive.google.com/open?id=0B9tqXyDsq9YIdkRhcVFXU2dEdnhINXR6Y3hza2Y5N… https://drive.google.com/open?id=0B9tqXyDsq9YIREd1OFZhNGZtRnN4aldtVU1mdk84N… As you can see the electron density fits very well the model. Why not a single residue gets a perfect correlation coefficient? (i.e. 1) Just curious. Thanks * phenix.real_space_correlation pdbfile mtzfile --detail="residue" > outpu

2 2

New bug in phenix.refine
by Aaron Oakley 23 Jun '19

23 Jun '19

Phenix.refine used to be able to handle a ligand covalently bound to cysteine if an appropriate cif dictionary was provided. This now seems to be broken. Re-running a job that used to work now fails. KeyError : 'link_CYS-MPS' Traceback: File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py", line 180, in run return_value = self.target() File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/libtbx/runtime_utils.py", line 75, in __call__ result = self.run() File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py", line 79, in run refine_object = self._run(args, callback) File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/runtime.py", line 92, in _run call_back_handler=callback) File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py", line 106, in run log=log) File "/usr/local/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py", line 224, in __init__ run_clash_guard=False) File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 1124, in setup_restraints_manager assume_hydrogens_all_missing = not self.has_hd()) File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5509, in geometry_restraints_manager log=self.log) File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5154, in construct_geometry_restraints_manager log=log, File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/monomer_library/linking_mixins.py", line 751, in process_nonbonded_for_links origin_id = origin_ids['link_%s' % key] File "/usr/local/phenix-1.15.2-3472/modules/cctbx_project/cctbx/geometry_restraints/linking_class.py", line 35, in __getitem__ raise e

2 1

Refining alternate conformation of duplex DNA
by ABHISHEK SUMAN 20 Jun '19

20 Jun '19

Hello All, I am solving a X-ray crystal structure of protein-DNA complex at 2.3 Angs. In my structure, it seems like the the duplex DNA is bound in two different conformations, and both the conformations are occupied in same density. I wish to know how to refine the alternative conformations of the DNA duplex in Phenix. In am using Phenix GUI. Thanks Abhishek *______________________________________________* *Abhishek Suman* *Research Scholar, PhD* C/o, Dr. Rajakumara Eerappa Macromolecular Structural Biology Group Department of Biotechnology R# 517,315, Academic Block - A Indian Institute of Technology Hyderabad Kandi 502 285 Sangareddy Telangana INDIA Contact: +91 91002 74548 (O) +91 80843 11898 (R) Email: abhisheks.iith(a)gmail.com ----------------------------------------------------------------- *Please don't print this e-mail or attachment unless necessary. Preserve trees on the planet.*

2 2

ISOLDE 1.0b3 release
by Tristan Croll 17 Jun '19

17 Jun '19

Dear structural biology community members, I am happy to announce that ISOLDE 1.0b3 is now live and available for installation via the ChimeraX Tool Shed. To get it, just download, install and run the ChimeraX 0.9 release version from http://preview.cgl.ucsf.edu/chimerax/download.html#release, then go to Tools/More tools… and find ISOLDE in the web page that appears. If you’re unfamiliar with what ISOLDE is about, in brief it’s an interactive model-building environment specifically tailored for the challenges encountered in fitting low-medium resolution maps. Find out more at https://isolde.cimr.cam.ac.uk. Best regards, Tristan What’s new in 1.0b3: - parallelised structure factor calculations (courtesy of ISOLDE’s sister plugin, ChimeraX_Clipper). - support for a wider range of chemical space (glycosylations courtesy of GLYCAM and various other post-translational modifications, and ~13,000 of the more common ligands in the wwPDB thanks to the work of Nigel Moriarty and David Case) - adaptive distance restraints (for reference model restraints and/or large-scale interactive flexible fitting – see https://isolde.cimr.cam.ac.uk/features-main/interactive-restraints/). - ability to fetch model and structure factors (as F/sigF, I/sigI or anomalous equivalents) straight from the wwPDB - interactive tutorials (run the command “isolde tut” on the ChimeraX command line) - various general usability and performance improvements.

1 0

NIH/NSF-Funded Visiting Research Specialist Position at the University of Illinois at Chicago
by Yury Polikanov 17 Jun '19

17 Jun '19

NIH/NSF-Funded Visiting Research Specialist Position in Structural Biology at the University of Illinois at Chicago The Polikanov Laboratory at the University of Illinois at Chicago (IL, USA) is looking for talented, skillful, and highly motivated researchers to fill the NIH/NSF-funded Visiting Research Specialist position to study the structure and function of the bacterial ribosome. The research in the Polikanov Laboratory is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. More information about Dr. Polikanov research can be obtained from the most recent publications ( https://www.ncbi.nlm.nih.gov/sites/myncbi/yury .polikanov.1/bibliography/50395623/public/?sort=date&direction=descending <https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.…>) or found on the laboratory web-page ( https://bios.uic.edu/bios/people/faculty/yury-polikanov <https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbios.uic.…>). The successful candidate will be involved in determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography techniques. Basic qualifications: • BS degree in chemistry, biochemistry, biophysics, or a related field is required; • MS degree or higher is preferred;• Minimum of 3 years of laboratory research experience is required; • Strong background in biochemistry and molecular biology is required; • Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); • Experience in structural biology (cryo-EM or X-ray crystallography) is not required but is highly desirable; • Experience in RNA biology field is not required but is highly desirable; The successful candidate is also expected to: • Act independently in terms of planning and executing the experiments; • Compile, analyze, and prepare data for publications; • Assist with training of graduate and undergraduate students. Interested candidates should submit their CV, cover letter, and contact information for three references at https://jobs.uic.edu/job-board/job-details?jobID=115527 <http://email.hiretouch.com/wf/click?upn=JvIYOHR1NyNpkeKMwd5M2xA-2FeX5NPtxOr…> by July 1, 2019. Cover letter should be describing how previous research accomplishments and scientific interests of a candidate fit with the scope of the research in the Polikanov Lab. The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans and individuals with disabilities are encouraged to apply. The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act *Jacquelyn DeLaurentis* *Human Resource Associate* *Department of Biological Sciences* *The University of Illinois at Chicago* *845 W Taylor St. * *3238 SES, MC 066* *Chicago, IL 60607* *(312) 996-2213* *jdelaur(a)uic.edu <jdelaur(a)uic.edu>* [image: UIC Logo]

1 0

wwPDB ligand validation updates
by John Berrisford 12 Jun '19

12 Jun '19

Hi Our recent update to the wwPDB validation reports provides much clearer validation information for ligands. We now include 2-dimensional diagrams of ligands, highlighting geometric validation criteria and, for structures determined by X-ray crystallography, 3-dimensional views of electron density. We also provide calculated electron density map coefficients which were used to generate the analysis in the validation reports. Initially, the updated-style reports will be available to in deposition, and publicly for newly released or updated PDB entries. The new features will be available for the whole archive following the next archive-wide recalculation validation reports. For more information, please visit https://www.wwpdb.org/news/news?year=2019#5cfa7992ea7d0653b99c87d0 Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/proteindatabank> http://www.facebook.com/proteindatabank <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

1 0

Phenix cryo-em tools workshop
by Ahmad Khalifa 07 Jun '19

07 Jun '19

Someone posted about a one day workshop for the cryo-em tools in Phenix. I can't seem to find this email, can someone please pass me a link to the workshop? Regards.

3 2

Postdoc Opening - Multi-Dataset Crystallography and Allostery - Keedy Lab, New York City
by Daniel Keedy 03 Jun '19

03 Jun '19

The Daniel Keedy Lab at the CUNY Advanced Science Research Center in New York City has an available position for a Postdoctoral Researcher starting immediately. The Keedy Lab aims to elucidate the conformational ensembles of proteins and to understand how they are shifted by perturbations, including mutations, protein:protein interactions, and ligands, to control function. We are especially interested in how “hidden” conformational ensembles drive differences in allosteric regulatory mechanisms for protein tyrosine phosphatases (PTPs), which are under-studied but biologically critical. To explore these questions, we are developing new multi-dataset approaches in X-ray crystallography that couple advances in automated data collection and multi-state modeling algorithms. For more information, visit our newly designed lab website: www.keedylab.org<http://www.keedylab.org> The ideal applicant should have a strong background in macromolecular X-ray crystallography, whether experimental, computational, or both. Experience writing or contributing to scientific software is also preferred. Candidates with other expertise in biophysics, computational biology, or related areas are also welcome to apply. The CUNY Advanced Science Research Center is a new cutting-edge research institution located in upper Manhattan in New York City -- the "greatest city in the world". The Structural Biology Initiative of the ASRC features seven tenure-track and research-track faculty members, pursuing diverse research problems using X-ray diffraction, cryo-EM, NMR, mass spectrometry, solution biophysics, and advanced microscopy. The ASRC is immediately adjacent to the New York Structural Biology Center, a consortium of CUNY and eight other New York academic institutions with world-class facilities, and 70 miles from Brookhaven National Laboratory, featuring the newly constructed National Synchrotron Light Source II, now the brightest synchrotron light source in the United States. The ASRC will also enjoy use of a new dedicated high-performance computing cluster starting this fall. You can officially apply for the position here: https://cuny.jobs/new-york-ny/research-associate-structural-biology-initiat… Feel free to contact Dr. Keedy directly at daniel.keedy(a)asrc.cuny.edu<mailto:[email protected]> with your CV and a brief description of your interests if you would like to discuss possible projects. Please pass this ad along to others who may be interested. Come join us in NYC! ~Daniel Keedy — Daniel A. Keedy, Ph.D. Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry and Chemistry Ph.D. Programs, CUNY Graduate Center www.keedylab.org<http://www.keedylab.org> | daniel.keedy(a)asrc.cuny.edu<mailto:[email protected]> | 212-413-3246

1 0

Integrating Pymol and coot in Phenix
by Darin Lory 29 May '19

29 May '19

PhenixGurus, I'm trying to get pymol and coot to run as viewers in Phenix 1.15.2-3472-final. I have PyMol version 2.3.2 installed and coot 0.8.9.1 "coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python". I have the executables in the Linux path as per the FAQ. When I click on the coot button I get another window "Coot is being started with Phenix extentions pre-loaded. Depending on the computer speed, it may take several seconds for the program to open". I get this message: $ phenix Already checked for new versions in last 24 hours, skipping /apps/packages/phenix/phenix-1.15.2-3472/build/../modules/phenix/phenix/command_line/start_coot.sh: line 37: /apps/packages/coot-installer/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/bin/0-coot-history.py: No such file or directory Then I click on the PyMol button and get this: Could not import runpy module Traceback (most recent call last): File "/apps/packages/pymol/lib/python3.7/runpy.py", line 15, in <module> import importlib.util File "/apps/packages/pymol/lib/python3.7/importlib/util.py", line 14, in <module> from contextlib import contextmanager File "/apps/packages/pymol/lib/python3.7/contextlib.py", line 5, in <module> from collections import deque File "/apps/packages/pymol/lib/python3.7/collections/__init__.py", line 27, in <module> from reprlib import recursive_repr as _recursive_repr File "/apps/packages/phenix/phenix-1.15.2-3472/conda_base/lib/python2.7/site-packages/reprlib/__init__.py", line 7, in <module> raise ImportError('This package should not be accessible on Python 3. ' ImportError: This package should not be accessible on Python 3. Either you are trying to run from the python-future src folder or your installation of python-future is corrupted. $ which coot /apps/packages/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/bin/coot $ which pymol /apps/packages/pymol/pymol $ which phenix /apps/packages/phenix/phenix-1.15.2-3472/build/bin/phenix My environment variables are: export PHENIX=/apps/packages/phenix export PHENIX_INSTALLER_DATE=080920070957 export PHENIX_VERSION=1.3 export PHENIX_RELEASE_TAG=final export PHENIX_ENVIRONMENT=1 export PHENIX_MTYPE=intel-linux-2.6-x86_64 export PHENIX_MVERSION=linux export PHENIX_USE_MTYPE=intel-linux-2.6-x86_64 source /apps/packages/phenix/phenix-1.15.2-3472/phenix_env.sh export PATH=${PATH}:${APPS_ROOT}/pymol:${APPS_ROOT}/pymol/bin:${APPS_ROOT}/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/bin:/usr/local/cuda-10.0/lib64:/usr/local/bin export LD_LIBRARY_PATH=${APPS_ROOT}/coot-Linux-x86_64-scientific-linux-7.6-pre-release-gtk2-python/lib:/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/lib:/usr/local/lib64:/usr/local/lib:${APPS_ROOT}/cryoEF_v1.1.0/lib:/usr/local/relion3/lib:${LD_LIBRARY_PATH} KIndly advise, -Darin

3 3

Can not decrease R-free value
by Pham, Hang 28 May '19

28 May '19

Dear all, I am refining my structures at 2.5 A. The model is well fitting in the electron density. I already add water and ligands. I’m trying these options (XYZ coordinates, real-space, TLS parameters, Individual B-factors, Optimize X-ray/stereochemistry weight, Optimize X-ray/ ADP weight, Reference model restraints, Use secondary structure restraints, Simulated annealing (Cartesian), Automatically correct N/Q/H errors) to refine the structure but the R-free still be high. The reference model is 98% identity with the structure that I’m building. After refining, the R-work always decrease while R-free increase. My last values for R-work is 0.2501 and for R-free is 0.3246. I’m lost and don’t know what to try more. Can anyone could explain me what happens here ? What others options that I could use to optimize R-free value ? Thank you in advance ! Hang Pham ------------------------------------------------------ Hang Pham, Ph.D Student, The Doucet Lab Centre Armand-Frappier Santé Biotechnologie Institut National de la Recherche Scientifique (INRS) Université du Québec Réseau International des Instituts Pasteur 531 Boulevard des Prairies Laval (Québec) H7V 1B7 CANADA Téléphone : (450) 687-5010, poste 4210 Site web: http://www.profs.inrs.ca/ndoucet/

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