- phenixbb - phenix-online.org

Molybdenum cofactor refinement
by Cristiano Mota 20 Nov '19

20 Nov '19

Hi all, I'm using phenix.refine to refine a structure of a Molybo-protein at 1.9Å. The MGD cofactors (molybdopterin guanine dinucleotide) are being refined with a weird distorted geometry causing some clashes. The Fo-Fc maps show that something is going wrong in the aromatic rings interatomic distances. I'm using the readyset to pick up MGD and metal restraints. Am I using the right protocol? Best regards, Cristiano Mota -- *Cristiano de Sousa Mota* Postdoctoral Researcher, Macromolecular Crystallography Group UCIBIO / FCT - Universidade Nova de Lisboa 2829-516 Caparica, Portugal (00351 212948300, ext 10962) http://xtal.dq.fct.unl.pt/

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Deadline Extended to December 9th
by Nick DeHaan 20 Nov '19

20 Nov '19

Hi PhenixBB, Thanks for sharing information about the AIMS Awards with your colleagues! Many have told us they really appreciated it. We’ve had requests for more time - so we extended the deadline to December 9th! For anyone with a protein target of interest, the AIMS Award program can help you discover new molecular tools, start new drug development efforts, and get published. The program is open to investigators, postdocs, and graduate students worldwide. We encourage you to check out our flyer for more information: Flyer <http://bit.ly/37oIrS3> You can apply directly on the website: atomwise.com/aims. Please don't hesitate to reach out with any questions! Best, Nick Nick DeHaan, MsE *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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cryo-EM density modification
by Tom Terwilliger 18 Nov '19

18 Nov '19

Hi Phenix cryo-EM users, For those of you trying out density modification for cryo-EM (phenix.resolve_cryo_em), the automatic estimation of resolution in the current version uses unmasked resolution instead of masked, in some cases resulting in running density modification at too low a resolution. Consequently it is best with this version if you specify your nominal resolution. To run it you can type: phenix.resolve_cryo_em half_map_1.ccp4 half_map_2.ccp4 \ seq_file=seq.dat resolution=3.5 or something like that. It requires the current nightly build to run. You might also want to wait just a short while and a version that has this and a few other bugs fixed, a GUI, full documentation, and an example dataset will be out (hopefully this week). The full description of the method is at https://www.biorxiv.org/content/10.1101/845032v1 Let me know of any problems or suggestions! All the best, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Differences in refinement statistics
by Chancievan Thangaratnarajah 18 Nov '19

18 Nov '19

Hello, I have noticed differences in the refinement statistics between two different Phenix versions (see attachments) even though I am using the same cryo-EM map and model as input. The most notable difference are rotamer outliers, which were 0 % in Phenix 1.16-3549 and now 6 % in Phenix 1.17-3660. I was wondering whether anyone has noticed a similar behaviour? Or is there something that I have missed? Best, Chancie.

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Error in sequence assignment
by Tom Terwilliger 17 Nov '19

17 Nov '19

Hi Nicholas, I'm afraid there isn't a way to say which sequence goes with which chain. I would suggest using the tool phenix.replace_side_chains. Give it 1 chain and 1 sequence and if they have the same length it should just put it in. If it doesn't work, try phenix.sequence_from_map which can do the same thing. Let me know if that doesn't do it! All the best, Tom T Date: Sun, 17 Nov 2019 17:07:16 -0500 From: Nicholas Gao <dominion146(a)GMAIL.COM> Subject: Specify chain assignment in sequence file for rebuild-in-place of phenix.autobuild Dear CCP4, I currently have an MR solution that has the wrong sequence. The pdb file of the solution contains 3 chains, and I'd like to use the rebuild-in-place functionality within phenix.autobuild to correct the sequence of all 3 chains. Phenix allows me to supply a sequence file as input for this job, it's not clear to me how I tell the program which sequence should be assigned to which chain. Anyone know how to do this? Sincerely, Nicholas Gao -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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RapiData at SSRL 2020 - application deadline extended by one week!
by Smith, Clyde 15 Nov '19

15 Nov '19

Hi all, We have extended the deadline for applications for a place at the RapiData 2020 @ SSRL workshop to next Friday, November 22 2019! There are still a few spots left, so get your application in! The workshop will be held from March 30 - April 4 2020 on the SLAC campus in Menlo Park, California. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, data collection strategies, X-ray light sources, X-ray detectors, data reduction, structure solution by MAD, SAD and molecular replacement, complementary methods (spectroscopy, small angle scattering and cryoEM). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. Successful applicants will be notified early in December 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in March 2020! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu csmith(a)slac.stanford.edu jwierman(a)slac.stanford.edu

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General interest
by John R Helliwell 14 Nov '19

14 Nov '19

Dear Colleagues, I imagine the two articles that I describe in my posting at the IUCr’s Forum will be of interest to the MX community. See:- https://forums.iucr.org/viewtopic.php?f=39&t=427 All best wishes, John Emeritus Professor John R Helliwell DSc

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Scientist job position at AbbVie
by Longenecker, Kenton L 13 Nov '19

13 Nov '19

Hi - I'd like to draw attention of interested candidates to the following job opportunity with full description to apply at: http://abbvie.referrals.selectminds.com/jobs/senior-scientist-i-ii-protein-… Company overview: AbbVie (NYSE:ABBV) is a global, research-driven biopharmaceutical company committed to developing innovative advanced therapies for some of the world's most complex and critical conditions. The company's mission is to use its expertise, dedicated people and unique approach to innovation to markedly improve treatments across four primary therapeutic areas: immunology, oncology, virology and neuroscience. In more than 75 countries, AbbVie employees are working every day to advance health solutions for people around the world. Job Description: The Structural Biology Group at AbbVie Headquarters in Lake County, Illinois, USA is seeking a highly motivated scientist to join our Structure-Based Drug Discovery team. The ideal candidate should have extensive hands-on experience in modern structural biology techniques and computational methods of molecular structure analysis. As part of multidisciplinary teams, the Senior Scientist will utilize X-ray crystallography techniques to identify ligands and provide insight to advance drug discovery targets through structure-based design. The successful candidate will contribute to drug discovery projects across the portfolio of AbbVie interests that also include therapeutic antibodies and novel biologics. ________________________________ Kenton Longenecker, Ph.D. Sr. Principal Research Scientist AbbVie R&D Discovery, DDST Structural Biology 1 N. Waukegan Road, AP10-LL North Chicago, IL 60064 OFFICE 847-938-1428 EMAIL kenton.longenecker(a)abbvie.com<mailto:%[email protected]> abbvie.com<http://www.abbvie.com> This communication may contain information that is proprietary, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any other dissemination, distribution, use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. ________________________________

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Submissions to the Computational Crystallography Newsletter – 30 NOV 19
by Nigel Moriarty 11 Nov '19

11 Nov '19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 2020 issue is 30 November 2019. 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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phenix-2Donline.org…>. 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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Postdoc Position in Berkeley
by Petrus Zwart 08 Nov '19

08 Nov '19

Dear All, We have two postdoc positions open in LBNL's Center for Advanced Mathematics in Energy Research Applications (CAMERA; https://www.camera.lbl.gov/) to work on a diverse set of problems in managing, cleaning and interpreting biophysical data ranging from microscopy to crystallography. https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88805 https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480 Feel free to contact me for more information. Regards Peter Zwart -- ------------------------------------------------------------------------ P.H. Zwart Staff Scientist Molecular Biophysics and Integrated Bioimaging & Center for Advanced Mathematics for Energy Research Applications Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 PHENIX: http://www.phenix-online.org CAMERA: http://camera.lbl.gov/ -------------------------------------------------------------------------

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