- phenixbb - phenix-online.org

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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intensity merging statistics for wwpdb deposition
by wtempel 03 Jul '19

03 Jul '19

Dear PHENIX users, how does one add merging statistics to PHENIX mmcif coordinates for deposition, assuming availability of AIMLESS logs and pre-merge intensities? Is this functionality implemented in PHENIX or CCTBX? Thanks. Wolfram Tempel

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r_work and r_free from an .mtz file containing Fobs and Fcalc
by Andre LB Ambrosio 01 Jul '19

01 Jul '19

Dear colleagues, Can Phenix calculate r_work and r_free from a .mtz file containing FP and FC_ALL (from PDB_REDO), without inputing the matching .pdb file? Many thanks in advance, -- Andre LB Ambrosio

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6th International Symposium on Diffraction Structural Biology: First Announcement
by Leighton Coates 01 Jul '19

01 Jul '19

Dear Colleague You are invited to the 6th International Symposium on Diffraction Structural Biology which will take place at the University of Osaka in Japan. Start Date: 17th Oct 2019 End Date: 20th Oct 2019 URL: https://isdsb2019.symposium-hp.jp/ The 6th International Symposium on Diffraction Structural Biology (ISDSB2019) is an international symposium organized by the Japan Society for the Promotion of Science, University-Industry Research Cooperative Research Committee, 169th Committee on Structural Biology using Diffraction Techniques. This symposium is positioned as an interface between academic researchers and industry researchers, as well as an interface between diffraction techniques and other related techniques in the field of structural biology. Symposium topics will include Macromolecular crystallography, CryoEM, software and databases, and drug discovery, registration and abstract submission for the symposium is now open and costs 25,000 Japanese yen for academics. A list of confirmed speakers for the symposium is currently being finalized; this will be posted on the symposium website within the next few days. Contact: Atsushi Nakagawa (Osaka University) Email: isdsb2019(a)gmail.com URL: https://isdsb2019.symposium-hp.jp/

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Mandatory PDBx/mmCIF format for crystallographic PDB depositions
by John Berrisford 01 Jul '19

01 Jul '19

>From today, July 1st 2019, submission of PDBx/mmCIF format files for crystallographic depositions to the PDB is mandatory. Refmac, Phenix.refine, and Buster programs can now output PDBx/mmCIF formatted files. For users of other structure determination/refinement software packages, the wwPDB provides stand-alone and web-based tools to convert legacy PDB format files into PDBx/mmCIF format: pdb_extract <http://pdb-extract.wwpdb.org/> and MAXIT <http://sw-tools.rcsb.org/apps/MAXIT/index.html> . More information on outputting and preparing PDBx/mmCIF format files for deposition can be found on the wwPDB website <https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files> . For more information, view the full news release at the wwPDB website <https://www.wwpdb.org/news/news?year=2019#5d17c1ceea7d0653b99c87e2> or contact the wwPDB on deposit-help(a)mail.wwpdb.org <mailto:[email protected]> . Regards John -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 <http://www.pdbe.org/> http://www.pdbe.org <http://www.facebook.com/proteindatabank> http://www.facebook.com/proteindatabank <http://twitter.com/PDBeurope> http://twitter.com/PDBeurope

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PEG as a polymer
by Felix Cat 29 Jun '19

29 Jun '19

Hi all, I'm working on a structure where I see extensive interaction of the protein with PEG (polyethylene glycol). The largest PEGs I can find in structures in the PDB with a quick search are around 12 EDO subunits long, and they're called "dodecaethanediol" or the like. I am seeing at least 20. Currently, I've built the PEG as a giant, single ligand, and generated a viable cif file for it using eLBOW with a SMILES string (very simple for PEG, you can imagine). I'm wondering if I might rather be able to handle it as a polymer of EDO subunits. I started to dig into that but got lost pretty quickly. I can't figure out how to create an automatically link-able EDO molecule, all with proper geometry, and I don't want to have to tell phenix.refine about 19+ custom linkages every time. (I've had to do that with N-linked acetylglucosamine moieties in the past.) Nate NUNC

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Real space refinement with helical symmetry
by Yangqi Gu 29 Jun '19

29 Jun '19

Hi all, I am trying to do a real space refinement with phenix and my map is a filament and I have monomer model and I would like to refine against my filament map. I am wondering how to impose the helical symmetry in this case? (I have a pseudo filament model by copying multiple subunits and aligned in Chimera using "fit in map"). Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus

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CaBLAM fixing and interpretation in comprehensive validation for cryo-EM
by Ahmad Khalifa 28 Jun '19

28 Jun '19

Hello, I would appreciate some insights on how to interpret the validation results under the CaBLAM tab and how to use it to fix my structure in Coot? What are the CaBLAM score, the Ca geometry score, the helix score and the 3-10 score? How to use the information under the secondary structure tab? In my protein for example, I see a lot of "try beta sheets", should I try to refine that segment using beta sheets restraints? Best regards.

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