- phenixbb - phenix-online.org

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 04 Jul '19

04 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 03 Jul '19

03 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/

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