- phenixbb - phenix-online.org

ASAPpdb - pledge to release data with preprints
by James Fraser 16 Dec '20

16 Dec '20

Fellow structural biologists - The revolution in publishing made possible by preprints calls for a re-evaluation of data disclosure practices in structural biology. While journal review processes take weeks, months, or even years, preprints allow researchers to rapidly communicate their findings to the community. However, withholding access to PDB files that accompany preprints inhibits the progress towards scientific discovery which preprints can enable. There is nothing more disappointing than reading a great preprint and not being able to open the coordinates and inspect the density! Sign the pledge to publicly release PDB files (and associated structure factor, restraint, and map files) with deposition of preprints here: https://asapbio.org/asappdb All the best, James PS> Apologies for the cross post to multiple bb's -- James Fraser - http://www.fraserlab.com - @fraser_lab jaimefraser(a)gmail.com // jfraser(a)fraserlab.com he/his/him (please do NOT use james.fraser(a)ucsf.edu)

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MicroED workshop 2020
by Johan Hattne 12 Dec '20

12 Dec '20

Dear all; We are pleased to announce the 6th MicroED workshop to be held on December 21, 2020. This will be a free virtual event. Please register at the following website to receive your link https://cryoem.ucla.edu/course Topics covered will include all aspects of microcrystal electron diffraction (MicroED) of diverse samples such as soluble proteins, membrane proteins, small molecules, natural products, and other materials. We will cover 1. Sample preparation methodologies 2. EPU-D for data collection 3. Camera systems and performance 4. FIB-milling procedures for soluble and membrane protein samples 5. Data analysis software, refinement, and structure solution The schedule is available on the registration page. // Sincerely; The organizing committee (Tamir Gonen, Brandon Mercado, Brent Nannenga)

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Submission Deadline on December 14th
by Tessa Van Grack 07 Dec '20

07 Dec '20

Hi PHENIX community, The AIMS Awards Fall 2020 application deadline is just one week away! For anyone with a protein target of interest, the AIMS Award program can help you discover new molecular tools, start new drug development programs, and get published. We encourage investigators, postdocs, and graduate students worldwide to apply. The AIMS Awards program provides non-profit researchers with virtual screening and compounds for physical testing at no cost. Collaborate with us to find novel active compounds for your protein target of interest. You can fill out the short application form directly on the website: atomwise.com/aims <https://hubs.la/H0z3sT80>. Please don't hesitate to reach out to me if you have any questions! Kind regards, Tessa *Tessa Van Grack, M.S.* Partnering Associate Atomwise <https://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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Re: [phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density
by Folmer Fredslund 03 Dec '20

03 Dec '20

Dear Igor There's a phenix bulletin board for question like this, which is where you should post the question. ( I crosspost here) I would choose to not do the real space refinement in phenix.refine during the last rounds of refinement of a model, when sidechain positions are essentially correct. I hope this helps Folmer tor. 3. dec. 2020 05.48 skrev Igor Petrik <petrik1(a)illinois.edu>: > I am refining a 1.71A X-ray structure with phenix refine. I have > everything modelled in - ~150 residues in the ASU and a heme - and my > R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out > that two of my sidechains have distorted geometries. One is a His, and > looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct > geometry, but the actual coordinates that phenix refine produce don't lie > in that density; there are significant difference map peaks showing that > the coordinates are in the wrong place. If I use real space refine in Coot > to put the coordinates back into the correct density and refine it again in > phenix, they get distorted again. > > What settings in phenix should I check to try to get it to properly refine > the coordinates? > > Thanks, > - Igor Petrik, PhD > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >

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Re: [phenixbb] 2x Postdoc positions and Lab Manager position
by Gordon Joyce 02 Dec '20

02 Dec '20

The Joyce Laboratory, Henry M. Jackson Foundation supporting the Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research have openings for two postdoctoral positions and a Lab Manager position in Structural Biology of Emerging Infectious Diseases. One postdoctoral position involves the structural and biochemical characterization of small molecule inhibitors against Emerging Infectious pathogens including SARS-CoV-2, as part of an integrated drug development pipeline at WRAIR. One postdoctoral position involves the structural and biochemical characterization of viral glycoproteins from Emerging Infectious pathogens including SARS-CoV-2 to enable vaccine development, antibody therapeutics and small molecule inhibitors. The Lab manager position will oversee day-to-day activities in the lab including lab inventory, ordering and routine mammalian cell culture and transient transfection. These positions offer a unique opportunity to gain extensive structural biology experience focused on vaccine and therapeutic development for pandemic prevention. Interested candidates should apply at the sites indicated below, or with a cover letter and a current CV directly to Gordon Joyce gjoyce(a)eidresearch.org<mailto:[email protected]> Postdoctoral Fellow: https://recruiting.ultipro.com/HEN1006HMJ/JobBoard/3a6861f3-0883-4466-8b7d-… Postdoctoral Fellow: https://recruiting.ultipro.com/HEN1006HMJ/JobBoard/3a6861f3-0883-4466-8b7d-… Lab Manager: https://recruiting.ultipro.com/HEN1006HMJ/JobBoard/3a6861f3-0883-4466-8b7d-… M. Gordon Joyce, Ph.D. Chief, Structural Biology The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF) In support of the Emerging Infectious Diseases Branch (EIDB) and the US Military HIV Research Program (MHRP) Walter Reed Army Institute of Research (WRAIR) 1N33, 503 Robert Grant Ave, Silver Spring, MD 20910 Office: 301-319-7528 Cell: 240-672-4311 https://eidresearch.org/our-team/m-gordon-joyce-phd gjoyce(a)eidresearch.org<mailto:[email protected]> ********************************************************************** This message contains information that may be confidential, privileged, proprietary, or otherwise protected. If you are not the intended recipient, notify the sender immediately and delete/destroy all copies of this message and any attachments. This message is not intended to constitute or include either an electronic record or an electronic signature unless otherwise specifically indicated.

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Power disruption (12/1 11 pm to 12/2 2 pm)
by Billy Poon 01 Dec '20

01 Dec '20

Hi everyone, Sorry for the short notice, but due to some electrical work in our building, several of the Berkeley servers will be shut down later tonight at 11 pm Pacific and will return tomorrow afternoon at 2 pm Pacific. This will affect: - The Phenix web site (http://phenix-online.org/) - 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. -- 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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alpha-Fold 2?
by lbetts0508 01 Dec '20

01 Dec '20

all - I just read the blurb in Nature Briefing about the DeepMind AI having made a big advance in the CASP protein fold prediction. Does it sound really transformational, does it work for membrane proteins - all the usual questions come to mind. Do we know enough yet about it? Signed an old protein crystallographer, L. Betts

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map_to_model input labels
by Schnicker, Nicholas J 20 Nov '20

20 Nov '20

Hi All, I'm trying to run map_to_model via command line for the first time (clearly) with an mtz file from an X-ray dataset. I have tried different iterations, but I can't seem to come up with the correct syntax for suppling the input labels. It gives me the list of available labels below, but what is the correct syntax to provide for input? Available labels: ['IMEAN,SIGIMEAN', 'I(+),SIGI(+),I(-),SIGI(-)', 'F,SIGF,DANO,SIGDANO,ISYM', 'F(+),SIGF(+),F(-),SIGF(-)', 'FreeR_flag'] Sorry I have checked the documentation, but still managed to fail. Thanks for your help, Nick

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Ensemble refinement with covalent ligands - bond length > 5Å
by Schulz, Eike-Christian 18 Nov '20

18 Nov '20

Dear all, I am running phenix.ensemble_refinement on a covalent protein-ligand complex providing the same parameter-files used for phenix.refine. I also included the .def and .cif files generated by phenix.ligand_linking. However, in quite a few of the ensemble structures, the covalent link exceeds 5Å, which is obviously wrong. How can I obtain ensemble structures with reasonable covalent bond length? Best, Eike ———————————————————————————— Dr. Eike C. Schulz Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 | 22761 Hamburg | Germany Building 99 (CFEL) | Office O2.101 Phone +49 (0)40 8998-6264<tel:%2B49%20%280%2940%208998-6264> | Fax +49 (0)40 8994-6264<tel:%2B49%20%280%2940%208994-6264> | Website www.mpsd.mpg.de<http://www.mpsd.mpg.de/>

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phenix.refine last cycle often break geometry for no obvious improvement
by Clement Degut 18 Nov '20

18 Nov '20

Hi, I regularly encounter this problem with phenix.refine, happened to me with several structures, at wildly different resolution, so as described in the title, phenix.refine seems to break perfect geometry in its last cycle (put 3 5 or 10 it's the last), for no obvious improvement in term of other metrics, actually getting the temporary file just before the last cycle had given me very good result in the past. Is there a reason for this behaviour? A way to get back PDB at a certain point of the refinements cycles would be really great actually. example of what I refer to: [image: image.png] Cheers, Clément Dégut PDRA Dr M Plevin's group University Of York

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