- phenixbb - phenix-online.org

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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