February 2021 - phenixbb - phenix-online.org

Autosol help: FOM is great but map is trash
by Alex Johnson 18 Feb '21

18 Feb '21

Hi Phenix team, I am attempting to phase a protein structure from SeMet-labeled crystals and have encountered some issues in using Autosol that appear unusual, as they have not been encountered by any members of my group. The short summary is that while I achieved great statistics from beam line collection and Autosol produces solutions with FOM (>0.4) from multiple crystals processed to ~2.4-3.0 A, the output maps are of poor quality and Autobuild can never build with Rfree <0.5. There is only one methionine for the ~30 kDa protein, but the crystals appear to have good anomalous signal with anomalous multiplicity >15 overall and delanon in the inner shell >0.5. There appears to be translational NCS and the dataset can be processed with good statistics in several space groups (P212121, P21212, P2122, etc) but this doesn’t solve the phase problem. The axis drops by half in processing in the P212121 versus P21212 space groups: from one crystal they are 48.37 101.56 110.39 90 90 90 (in P212121) and 101.62 48.35 55.19 90 90 90 (in P21212). If anyone in the community has encountered similar problems please let me know! I am all ears to any possible solutions and am also installing additional methionine for labeling but unsure whether this will overcome the other issues. Thanks, Alex Johnson Postdoc, Kranzusch lab, Dana-Farber Cancer Institute algejohnson(a)gmail.com <mailto:[email protected]>

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Post-Doctoral Position at the University of Illinois to Study Ribosome Structure
by Yury Polikanov 16 Feb '21

16 Feb '21

*Post-Doctoral Position in Structural Biology at the University of Illinois at Chicago (UIC) to Study the Structure and Function of the Ribosome* The Polikanov Laboratory at the University of Illinois at Chicago (IL, USA) is looking for a talented, skillful, and highly motivated researcher to fill the available *NIH-funded Post-Doctoral Scholar *position to study the structure and function of the bacterial ribosome. The research in the Polikanov Laboratory is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. More information about Dr. Polikanov research can be obtained from the most recent publications (*https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/50395623/public/?sort=date&direction=descending <https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/503…>*) or found on the web-page (https://bios.uic.edu/bios/people/faculty/yury- polikanov). The successful candidate will be involved in the determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography and potentially cryo-EM techniques. *Basic qualifications:* - PhD in chemistry, biochemistry , biophysics, or a related field; - Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); - Experience in structural biology (X-ray crystallography or cryo-EM); - Experience in the RNA biology field is not required but highly desired; *The successful candidate is also expected to:* - Act independently in terms of planning and executing the experiments; - Compile, analyze, and prepare data for publications; - Assist with training of graduate and undergraduate students. Review of applications will begin immediately and will continue until the position is filled. Interested candidates should apply by 04/16/2021 using the following link: https://jobs.uic.edu/job-board/job-details?jobID=142760 or email directly to Dr. Polikanov - yuryp(a)uic.edu. Please make sure to include CV, cover letter, and contact information for three references. *For full consideration, in **the cover letter, describe** how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group.* *The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans, and individuals with disabilities are encouraged to apply.* *Offers of employment by the University of Illinois may be subject to approval by the University’s Board of Trustees and are made contingent upon the candidate’s successful completion of any criminal background checks and other pre-employment assessments that may be required for the position being offered. Additional information regarding such pre-employment checks and assessments may be provided as applicable during the hiring process.* *The University of Illinois System requires candidates selected for hire to disclose any documented finding of sexual misconduct or sexual harassment and to authorize inquiries to current and former employers regarding findings of sexual misconduct or sexual harassment. For more information, visit **https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899 <https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899>*

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postdoctoral position in cryo-EM at LMB in Jan Löwe's group
by Jan Löwe 16 Feb '21

16 Feb '21

Dear all, My group has a grant-funded job opening for a postdoctoral structural biologist to work on problems in archaeal and bacterial cell biology. The aim is to understand cell division and vesicle formation at the molecular or even atomic scales. The work will involve state-of-the-art cryo-EM, biochemistry and tomography (and who knows, maybe even crystallography and/or NMR). We are surrounded here at LMB by many experts and a lot of exciting instrumentation, and given the current state of the project, only the sky (and our imagination) is the limit. Please find the job advert here: https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-… <https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-…> Please do get in touch if you would like to know more before applying. Best wishes, Jan Jan Löwe MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH UK email: jyl(a)mrc-lmb.cam.ac.uk website: http://www2.mrc-lmb.cam.ac.uk/groups/jyl

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Re: [phenixbb] rotamer outlier and clash socre
by Pavel Afonine 14 Feb '21

14 Feb '21

Hello Pan, """ I refined a cryo-EM data with 3.2 angstrom, the model fit well with the map, but the rotamer outlier is too high, about 8%. How can I decrease the value of rotamer outlier by realspace.refinement in Phenix GUI, and no need to adjust the residues one by one in Coot? """ if you used latest version of Phenix, which is dev-4146 as of today: http://phenix-online.org/download/nightly_builds.cgi?show_all=1 then this is not expected, because phenix.real_space_refine has built-in ability to detect which residues need a fix and does an exhaustive grid-search in chi-torsion angle space to optimize it against the map and local environment. If this happened using the latest version of Phenix, then this is an indication to me that something has gone wrong and we need to investigate. For this I'm asking to send all input files. Residues that phenix.real_space_refine was unable to fix for whatever reason are best to fit manually in Coot. And I can't agree more with Tristan -- all the great tools and automation are to help you not substitute you! So, checking manually is important! """ Another question is the value of clash score are also too high. """ You did not tell us the value, so no answer here! A general guidance: the lower the better, but zero is not the goal. """ When I set the nonbonded_weight to 10000 """ According to study we conducted recently: http://phenix-online.org/presentations/nb_weight.pdf this unlikely to be a great idea. Pavel

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rotamer outlier and clash socre
by xiaowp82＠hotmail.com 14 Feb '21

14 Feb '21

Hello everyone I refined a cryo-EM data with 3.2 angstrom, the model fit well with the map, but the rotamer outlier is too high, about 8%. How can I decrease the value of rotamer outlier by realspace.refinement in Phenix GUI, and no need to adjust the residues one by one in Coot? Another question is the value of clash score are also too high. When I set the nonbonded_weight to 10000, the clash score get better, but the value of rotamer outlier get worse. The high clash score maybe due to including hydrogens for refinement? Can I exclude hydrogen for refinement and how to do? Thanks ! Pan xiaowp82(a)hotmail.com

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Phenix ligand identification resolve was not able to finish on the first cycle
by Ahmad Khalifa 14 Feb '21

14 Feb '21

Hello, I want to use phenix.ligand_identification to identify a ligand. I used chimera's volume eraser to erase everything except for the ligand density. I then converted it to mtz. in the phenix.ligand_identification gui, I set reflection data type to difference map. When I ran the job, I got a lot of "Sorry, resolve was not able to finish on the first cycle". Regarding the mtz, I have to contour the map to 170rmsd to visualize it in coot, so something have to be wrong. I appreciate any input. Best regards.

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on phenix uninstall
by Smith Lee 13 Feb '21

13 Feb '21

Dear All, In order to install new version of phenix, should I uninstall the older version of phenix first? If needed, what are the command to uninstall the windows version of phenix and to uninstall the linux version of phenix? Smith

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The weblinks for the Daresbury Laue software source code and information
by John R Helliwell 12 Feb '21

12 Feb '21

Dear Colleagues, The weblinks for the Daresbury Laue software source code and information have become hidden from a simple google search. This short article at IUCr Journals makes clear where the software source code and information can now be found. See:- https://journals.iucr.org/s/issues/2021/02/00/me6120/index.html Best wishes, John Emeritus Professor John R Helliwell DSc

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unable to run coot
by Badmalia, Maulik 12 Feb '21

12 Feb '21

hello team phenix, I hope this email finds you well. I recently downloaded phenix for analysing our cryoEM data, before moving to the data analysis I decided to try the tutorial. I decided to use the autosharpen option first, I was able to access the tutorial but when I clicked on coot I repeatedly got a message saying that "Sorry: the 'coot' command could not be located. We have installed Coot to run on a CentOS platform and has the latest version of Coot on the system. I am a novice with linux and phenix. So any help in this regard would be highly appreciated. Do let me know if you have any questions. Regards, Maulik Maulik D. Badmalia Postdoctoral Researcher Laboratory of Medicinal Biophysics Alberta RNA Research and Training Institute Dept. of Chemistry & Biochemistry University of Lethbridge, Lethbridge, AB, Canada

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Re: [phenixbb] unable to run coot
by Werther, Rachel A 11 Feb '21

11 Feb '21

Hello Maulik, Sometimes uninstalling Xquartz and reinstalling it will correct the link between Phenix and Coot, particularly after computer updates. Best of luck, Rachel Rachel Werther / she & her pronouns / Research Technician III / Campbell Lab / Lab A3-201 / 206-667-4189 / Basic Sciences Division / Fred Hutchinson Cancer Research Center / rwerther(a)fredhutch.org<mailto:[email protected]> From: <phenixbb-bounces(a)phenix-online.org> on behalf of "Badmalia, Maulik" <maulik.badmalia(a)uleth.ca> Date: Thursday, February 11, 2021 at 3:37 PM To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] unable to run coot hello team phenix, I hope this email finds you well. I recently downloaded phenix for analysing our cryoEM data, before moving to the data analysis I decided to try the tutorial. I decided to use the autosharpen option first, I was able to access the tutorial but when I clicked on coot I repeatedly got a message saying that "Sorry: the 'coot' command could not be located. We have installed Coot to run on a CentOS platform and has the latest version of Coot on the system. I am a novice with linux and phenix. So any help in this regard would be highly appreciated. Do let me know if you have any questions. Regards, Maulik Maulik D. Badmalia Postdoctoral Researcher Laboratory of Medicinal Biophysics Alberta RNA Research and Training Institute Dept. of Chemistry & Biochemistry University of Lethbridge, Lethbridge, AB, Canada

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