- phenixbb - phenix-online.org

MicroED Workshop 2019
by Johan Hattne 13 Aug '19

13 Aug '19

The Gonen Laboratory will hold the 5th MicroED Workshop in 2019. The workshop will be held at the MicroED Imaging Center at the UCLA David Geffen School of Medicine during December 9-12, 2019 and is open to both academia and industry. Space is limited and historically, the workshop is typically oversubscribed. Topics covered: * MicroED conception, practice and future opportunities * Electron optics for MicroED * Microscope alignment and calibration for MicroED * Sample preparation: protein and organic/inorganic materials, small molecules * Data collection for both protein and small molecules * Data analysis software, structure solution, and refinement * Choice of electron microscope hardware and cameras * MicroED publication standards: what statistics to include and when is your structure publication-ready? Further application information is available from https://cryoem.ucla.edu/pages/Workshop The application deadline is October 1, 2019. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095

1 0

Clipper updates for C++11
by Billy Poon 12 Aug '19

12 Aug '19

Hi everyone, As part of making CCTBX-based software compile with C++11, it looks like we need to update our checkout of clipper to the latest version. http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html As a side note, is this a feature that is widely used? If not, we can disable the downloading of the clipper source files. Also, in addition to this post on the bulletin board, I have started an issue on Github (https://github.com/cctbx/cctbx_project/issues/379). Feel free to comment on any of these forums. -- 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

1 0

Setting master for finding NCS operators from PDB
by Ahmad Khalifa 12 Aug '19

12 Aug '19

Hello, I have a macro-molecular structure that I want to find the NCS rotation/translation for. Does the program automatically set the first alphabetical letter chains as master's?! Is there a way to specify which chains I want as master? Regards.

1 0

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> -------------------------------------------

1 0

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

1 0

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

1 0

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/

1 0

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

1 0

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

2 1

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

1 0

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

1 0

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

2 1

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

1 0

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

4 5

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.

2 1

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

1 0

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.

1 0

CryoEM specialist positions open at CSIR-CCMB, India
by Rukmini Raju 22 Jul '19

22 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) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

1 1

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.

2 2

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

2 1

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

1 0

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.

2 1

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.

2 1

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.

2 1

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 ] --

1 0