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Refinement of two co-factors at the same position
by Kornelius Zeth 12 Apr '17

12 Apr '17

Dear all, I'm trying to refine the occupancy and position of two co-factors iron (III) and FEO (Fe-O-Fe) in a crystal structure. The iron (III) is placed with some occupancy on one of the iron positions in FEO. If I refine them together in Phenix with low occ phenix.refine moves the atoms apart. What is the best way of dealing with this problem? Thanks and best wishes Kornelius

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Symposium on Understanding Biology through Structure, May 13-17, 2017, Santa Fe
by Wladek Minor 12 Apr '17

12 Apr '17

Dear Colleagues, As a member of the organizing committee of "Understanding Biology through Structure", I'd like to encourage you to come to Santa Fe May 13-17 to attend this exciting Symposium. In addition to an exceptional set of talks including X-ray crystallography, cryo-EM, biochemical and biophysical methods, the Symposium will emphasize interactions between junior and senior researchers. We hope that this will present a special opportunity for junior researchers to present posters and meet senior scientists, for senior researchers to meet the next generation of structural biologists, and for all to discuss science in an informal setting. The meeting website is at https://conferences.newmexicoconsortium.org/conferences/ubts_17 and the program can be seen at https://conferences.newmexicoconsortium.org/conferences/ubts_17/program Looking forward to seeing you there, Wladek Minor -- Dr. Wladek Minor Harrison Distinguished Professor Department of Molecular Physiology and Biological Physics Phone: 434-243-6865 Fax: 434-243-2981 http://krzys.med.virginia.edu/CrystUVa/wladek.htm US-mail address: Department of Molecular Physiology and Biological Physics University of Virginia PO Box 800736, Charlottesville, VA 22908-0736 Fed-Ex address: Department of Molecular Physiology and Biological Physics 1340 Jefferson Park Avenue University of Virginia Charlottesville, VA 22908 ----

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Fwd: [ccp4bb] Join the editorial team of IUCr Journals
by Randy Read 07 Apr '17

07 Apr '17

Just in case anyone on the Phenix BB doesn't read the CCP4 one! Best wishes, Randy Read > Begin forwarded message: > > From: Louise Jones <lj(a)IUCR.ORG> > Subject: [ccp4bb] Join the editorial team of IUCr Journals > Date: 7 April 2017 at 13:23:42 BST > To: CCP4BB(a)JISCMAIL.AC.UK > Reply-To: Louise Jones <lj(a)IUCR.ORG> > > Dear All > > We are now seeking a number of new Editors and Co-editors for IUCr Journals, including our biological journals > > > > Acta Crystallographica Section D, Structural Biology > and > Acta Crystallographica Section F, Structural Biology Communications > > Full details are available at > http://www.iucr.org/news/notices/announcements/chesternotice_2017_04 > > Best wishes > Louise > _____________________________________________________ > > Louise Jones > Managing Editor > Acta Cryst. D and Acta Cryst. F > International Union of Crystallography > ________________________________________________________ ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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New Phenix tutorial videos
by Dorothee Liebschner 07 Apr '17

07 Apr '17

Dear Phenix users, We uploaded more videos to the Phenix Tutorial YouTube channel <https://www.youtube.com/channel/UCcdI0hfHngWAZLJWynxPQWg>: - Basic Phenix eLBOW tutorial - How to run Phaser-MR from the Phenix GUI - Explaining the atom selection syntax To give us feedback, write to tutorials(a)phenix-online.org or use the comment section in YouTube. If you are eager to see a tutorial about a certain (Phenix-related) topic, don't hesitate to tell us. Further info: To see subtitles, hit the cc (closed captions) button in the right bottom of the video screen. Subscribe to the channel to see the tutorial videos in your YouTube subscription feed. To get notifications about new videos, tap the bell button (next to the "subscribe" button). Best wishes, The Phenix team

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What happened with Rfree between dev-2376 and now?
by Mark Saper 29 Mar '17

29 Mar '17

Hi all, I’ve been running some tests with the current dev and released versions of Phenix. If I run the same job (same input files, same parameters), the current versions consistently result in Rfree values ~1% more than Phenix version dev-2376! What changed between then and now? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

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Note that R-free numbers are different than a year ago.
by Mark Saper 26 Mar '17

26 Mar '17

In July 2016, I finished a refinement with Phenix dev-2376 with these final stats start final --------------------------------------- R-work: 0.1982 0.2007 R-free: 0.2376 0.2367 RMS(angles): 0.55 0.45 RMS(bonds): 0.003 0.002 Today, I reran the exact same parameter file and input files with Phenix dev-2712: start final --------------------------------------- R-work: 0.2073 0.2037 R-free: 0.2445 0.2442 RMS(angles): 0.55 0.45 RMS(bonds): 0.003 0.002 R-free values are now higher than they used to be. This fact was also flagged when I ran Table 1 today. -Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

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help with pdbtools
by Edward A. Berry 25 Mar '17

25 Mar '17

1. I'm trying to use pdbtools and I don't quite get the syntax. How can I specify the output file name on the command line? these don't work: phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 output file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --output file_name = shake1.pdb phenix.pdbtools 2chr_refine_001.pdb sites.shake=0.5 --file_name = shake1.pdb phenix.pdbtools --output file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5 phenix.pdbtools output.file_name = shake1.pdb 2chr_refine_001.pdb sites.shake=0.5 2. for the "shake" operation, is there a random seed so that it comes out differently each time? (If I do this five times with different output file names, will they all be the different?)

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DNA double helix through crystal symmetry
by wtempel 25 Mar '17

25 Mar '17

Hello, how could one restrain DNA base pairing across a crystallographic axis? Are secondary_structure.nucleic_acid restraints "symmetry-aware"? Thank you. Wolfram Tempel

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Berkeley Server Downtime (3/23 - 3/24)
by Billy Poon 24 Mar '17

24 Mar '17

Dear all, On Thursday, March 23, our servers will be shut down starting at 5:00 pm Pacific for some emergency electrical work near our building. We expect that the servers will be available the next day (3/24) by 1:00 pm Pacific. There is a possibility that the outage will last longer. This will affect, - 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/) 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 and the short notice. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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options in phenix.merging_statistics
by Murpholino Peligro 23 Mar '17

23 Mar '17

Hello. I was wondering what is the normal situation where one should click the boxes marked as "Keep anomalous pairs separate in merging statistics" (option1) and/or "Use internal variance of the data in the calculation of the merged sigmas" (option2)? I am asking because it looks like it is detrimental to the statistics, as you can see in the file attached (CSV file with 4 columns for no options, option1, option2 and option1&2). Thanks in advance. MP

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