- phenixbb - phenix-online.org

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 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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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 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) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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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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