- phenixbb - phenix-online.org

How to compare between electron density maps?
by Murpholino Peligro 12 May '20

12 May '20

I want to compare electron density features of map A from protein A and map B from protein B... Because each map has a different rmsd level... ...what is the best way to compare electron density between maps? Is there a way to normalize maps or something like that? Thanks

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Is there a way to search the phenixbb mailing list archive?
by Murpholino Peligro 11 May '20

11 May '20

With the ccp4bb at https://www.jiscmail.ac.uk/cgi-bin/webadmin I can search for a term in the archive. Is there something similar in the phenixbb? Thanks Or... is there a way to wget all the gz files?

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Online Course on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 11 May '20

11 May '20

ORNL Online Course on Neutron Scattering Applications in Structural Biology (https://conference.sns.gov/event/217/) June 1 - June 5, 2020 2:00 pm - 5:30 pm EST Registration (free) is now open and will close May 17, 2020. This online course is designed for graduate students, post-doctoral researchers and faculty with knowledge of structure and function of biological macromolecules but with limited to no experience with neutron sciences. The course will cover the basics of deuterium labeling, small angle neutron scattering, neutron reflectometry, neutron spectroscopy, neutron imaging and neutron crystallography. Instrumentation, sample preparation, data collection and processing will be introduced for each neutron technique.

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Boost 1.70 update for cctbx
by Billy Poon 09 May '20

09 May '20

Hi everyone, There is currently a pull request for cctbx that will update Boost to 1.70 ( https://github.com/cctbx/cctbx_project/pull/409). The update enables support for Python 3.7 and 3.8. The plan is to merge this next Friday, May 8, at 3 pm Pacific. After merging, developers should delete the build/lib/*boost* files and build/boost directory so that any remnants of the old Boost are removed and then rebuild. Let me know if you have any questions. Thanks! -- 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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Phenix installation
by Sam Tang 06 May '20

06 May '20

Hi I am installing Phenix on a Fedora 30 station. It complains line 15: /usr/bin/python: No such file or directory. I have checked that there is python3.7.3 pre-loaded. So did I miss anything obvious...? Brs Sam

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Ligand refinement - geometry does not fit density
by Schulz, Eike-Christian 04 May '20

04 May '20

Dear all, I am refining a structure with a simple ligand in phenix 1.14. The ligand is present in 2 conformations at approx. equal occupancy. Refinement of the 2 conformations runs smoothly, but 2 problems occur 1. One of the ligand atoms is placed out of the electron density after refinement. The geometry file (via elbow) is present during refinement. The atom is not in an extreme position or clashes with anything else. 2. After refinement the ligand conformation cannot be changed in coot, although I import the cif dictionary. Any advise ? Best, Eike

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Phenix 1.18 RSR runtime
by Hannah Bridges 02 May '20

02 May '20

Dear Phenix developers, We have updated to phenix version 1.18-3845-000 and found that realspace refinement (5 cycles) with minimization global, local grid search and ADP is taking about 36 hours, compared to ~ 1hr in versions 1.17 and 1.16. The slow step is the local grid search which is taking >6 hours each cycle. We are very glad for the option to run the job detached, but I wondered if this sort of timing was expected for this version? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

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off-topic; suggestions for 96head liquid handler
by Georg Mlynek 30 Apr '20

30 Apr '20

Dear Scientific community, we have lend over Viaflow96 liquid handler (used for pipetting 35-50 uL in 96 well crystallization plates) to our Covid -19 Diagnostics Initiative. As we believe that this story will be ongoing for some longer time I am looking for a new 96 head liquid handler. We are happy with the Viaflow and have two heads 10-300 uL; 0.5-12.5 uL. However one tip box (96 tips for the 10-300 uL) is about 4 €. This compares to ~1 € for the refilling racks we use for our single channel pipettes (It is said that boxes have to be more rigid, because of pressure during tip loading). Therefore if you have a 96 head liquid handler for volumes of 20-60 uL where cheap tips can be used (automation not necessary) please write me. Many thanks in advance, best regards, Georg.

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Computational Crystallography Newsletter (CCN) release and submissions
by Nigel Moriarty 28 Apr '20

28 Apr '20

Folks Recent world events have affected many things including the timely release of the CCN. Please consider this the Shelter-In-Place edition. Many of you will be involved in SARS-CoV-2 research and the CCN for July 2020 can be a vehicle for publishing the more community interest details. The deadline for submissions is 1 JUN 2020. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. 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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Open postdoc positions in the Gonen lab
by Johan Hattne 26 Apr '20

26 Apr '20

Dear all; We would like to draw your attention to two HHMI-funded postdoc positions in the laboratory of Tamir Gonen at the University of California, Los Angeles. The first position concerns the biochemistry of membrane proteins, the second is focused on computational methods development. For further information, as well as application instructions, see the links below. Biochemistry https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobin… Programming https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobin… // Best wishes; Johan

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