Re: [ccp4bb] High Rfree in last Shell
Also, values in parentheses (high-res shell) depend on how you (the program you use) do binning. Different programs do it differently and so these values can vary quite substantially. With a little of trial-and-error effort choosing the binning one can make these values farther or closer to overall R. To me this is a hint that these numbers are not very useful. A plot R (completeness, ..) vs resolution is much more useful than the values for an arbitrarily defined resolution bin! Pavel On Wed, Apr 17, 2019 at 12:57 AM Jan van Agthoven wrote: > Hi everyone, > I’m trying to publish two structures at 3.1Å resolution with the following > refinement statistics: > > Resolution range (Å) 49.2-3.1 > 49.3-3.1 > *R*factor (%)24.0 (32.4) > 23.4 (32.0) > *R*free (%) 26.6 (29.2) > 26.3 (31.6) > > *Data collection* > > Completeness 100 (100) > 100 (100) > > Redundancy6.9 (7.0) > 6.2 (6.3) > > Molecules in asymmetric unit 1 > 1 > > Average* I*/σ 14.1 (1.7) > 15.3 (2.0) > > *Rmerge *(%) 14.9 (100) > 12.7 (100) > > *Rmeas* (%)16.2 (100) >13.9 (100) > > *Rsym* (%) 6.2 (68.6) >5.5 (57.1) > Wilson *B*-factor 65.6 > 62.7 > > I’ve been told that the Rfree factor in the* last shell* are too high. > Does anyone know how I can improve these Rfree factors other then cutting > the resolution, which already is rather low? > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Phenix version 1.15 released
The Phenix developers are pleased to announce that version 1.15 of Phenix is now available (build 1.15.2-3472). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for this version: New and improved tools - New algorithm for phenix.map_to_model is faster and builds longer chains - phenix.trace_and_build can build protein into maps at resolutions as low as 4.5 A - phenix.fix_insertions_deletions can build models in places where the map is poor - phenix.refine_ca_model for optimizing C-alpha only models - phenix.comparama for generating Kleywegt-like plots that show how residues moved in the Ramachandran plots before and after refinement - eLBOW can find unique instances of a ligand from the PDB and optionally create Polder OMIT maps - Updated structural library for phenix.structure_search - Updated ligand library for phenix.ligand_identification - Improved reporting of cis-peptides for residues with altloc atoms - Output of mmCIF format files by default by major tools: phenix.refine, phenix.real_space_refine, phenix.pdbtools - Bugfixes in Phaser-2.8.3 Other improvements - Updated mmCIF support (stuct_conn loop, ligand restraints, sequence) - phenix.refine, phenix.real_space_refine, and phenix.pdbtools will also output models in mmCIF format by default - Dependencies are now based on conda packages, which will be more compatible with new operating systems and will improve consistency across all platforms (macOS, linux, Windows) - Bug fixes For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: h...@phenix-online.org and b...@phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area 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 [ lbenve...@lbl.gov ][ 1-510-495-2506 ] -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Scientist - CryoEM position at Frederick National Laboratory for Cancer Research
Hello everyone, The Frederick National Laboratory for Cancer Research (operated by Leidos Biomedical Research for NCI) is looking for a Scientist with experience in single-particle cryo-electron microscopy to work on multiple large protein-protein complexes in RAS biology. The Frederick National Laboratory hosts National Cryo-EM facility which allows relatively easy access to high-end cryo-electron microscopes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4=leidosbiomed=465 Best wishes, Dhirendra Simanshu To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] SFX beamline scientist position at the SwissFEL
Dear all, I would like to draw your attention to a tenure-track beamline scientist position in macromolecular crystallography group at the Photon Science Division, Paul Scherrer Institut (https://www.psi.ch/macromolecular-crystallography/). This position offers a unique opportunity to develop and operate a dedicated serial femtosecond crystallography (SFX) station at the SwissFEL. Detailed information and the online application portal can be found at https://www.psi.ch/pa/stellenangebote/2000. Best regards, meitian __ Meitian Wang Head of Macromolecular Crystallography Group Photon Science Division Paul Scherrer Institut +41 56 310-4175 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] analytical gel filtration columns
Hi Mohinder, if you are up to trying something new the monolithic columns by Biaseparation (analytical or prep) are well suited for big molecules / particles and worked very well for me. The fittings work with the GE chromatography instruments. https://www.biaseparations.com Good luck, Bärbel -- Bärbel Blaum, PhD Inthera Bioscience AG Einsiedlerstrasse 34 CH-8820 Waedenswil Switzerland E-Mail: baerbel.bl...@intherabio.com Phone: +41 43 477 94 72-- Von: CCP4 bulletin board im Auftrag von David Blum Antworten an: David Blum Datum: Mittwoch, 17. April 2019 um 21:48 An: Betreff: Re: [ccp4bb] analytical gel filtration columns Mohinder, You could also try HPLC where you should get better results due to more theoretical plates. One option would from Phenomenex. 10E6A Phase Information · Molecular Weight Range: 60 K - 10,000 K https://www.phenomenex.com/Products/HPLCDetail/phenogel David L. Blum, Ph.D. Bioexpression and Fermentation Facility | Director Master of Biomanufacturing and Bioprocessing | Director 120 Green Street | Life Sciences Bldg rm A414A | Athens, GA 30602 706-542-1035 | b...@uga.edu | bff.uga.edu | biomanufacturing.uga.edu On Wed, Apr 17, 2019 at 11:11 AM Mohinder Pal wrote: Dear all, I would like to gel filter a multi protein complex (1.4MDa) as the final purification step. I have tried tandem Superose 6 columns and this complex elutes close to void volume as it is a very elongated molecule. I was wondering if someone could suggest different analytical columns for better resolution as I plan to add more components to this existing complex. Best wishes, Mohinder Pal -- "Whatever you’re meant to do, do it now. The conditions are always impossible.” Doris Lessing -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
