July 2019 - phenixbb - phenix-online.org

Real space refinment keeps messing up my taxol conformation
by Ahmad Khalifa 21 Jul '19

21 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 19 Jul '19

19 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 19 Jul '19

19 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 18 Jul '19

18 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 17 Jul '19

17 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 14 Jul '19

14 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 14 Jul '19

14 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 13 Jul '19

13 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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