- phenixbb - phenix-online.org

Twinned data with Phaser
by Thomas, Leonard M. 25 May '21

25 May '21

Hello, I have been working on a structure for a very long while. We have a number of data sets with the good ones mostly around the 3.1-3.2 A range. I do have a determination of the structure but would like to see if I can get the structure determined with a slightly higher resolution data set at around 2.7 A. Problem is the 2.7 data is twinned. Are there settings in Phaser to handle twinned data or is the twinning only handled during refinement? Thank you for any advice, outside of forgetting about the twinned data. Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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Problems with sharpening in Autosharpen
by Carlos HENRIQUE FERNANDES 25 May '21

25 May '21

Dear all, I am facing some problems with sharpening in Autosharpen. My current map is about 3.2 Å resolution, which I obtained after CTF-Refinement and Polishing in Relion. When I use Autosharpen in default parameters, it tells me that are applied an overall Bsharp applied of 220.34 and a final Biso of 87.42; but very little sharpening is done; I was unable to observe a typical helices sharpening at this value of resolution. I did some tests setting progressive Bsharp values (240; 260; 280; 300), but I am still unable to visualize a typical helices sharpening. Has anyone had problems like that? Any tips? Thanks in advance, Carlos.

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Exclude atoms from real space refinement
by Florian Nachon 23 May '21

23 May '21

Hello, I want to exclude a residue from XYZ refinement, but I noticed that my atom selection "not (chain A and resid 100)" is ok for reciprocal-space, but not real-space? Someone encounter a similar problem 10 years ago: http://www.phenix-online.org/pipermail/phenixbb/2012-December/019297.html Is it a known bug? Any clues? Thanx in advance — Florian

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Fwd: [SRCC #47733] Fwd: Phenix GUI showing unreadable squares
by Dong-Hua Chen 19 May '21

19 May '21

Hi All, I asked Stanford cluster admin and he is questioning the CentOS version incompatibilities (see the following). Any suggestions? Thanks Dong-Hua ---------- Forwarded message --------- From: Kilian Cavalotti <srcc-support(a)stanford.edu> Date: Thu, May 13, 2021 at 12:20 PM Subject: Re: [SRCC #47733] Fwd: [phenixbb] Phenix GUI showing unreadable squares To: <donghua.chen(a)gmail.com> Hi Dong-Hua, It looks like the software is built for CentOS 6.10, while Sherlock is running CentOS 7.x, so incompatibilities are likely. Is there a way to rebuild it from source. maybe? Cheers, -- *Kilian Cavalotti* Stanford Research Computing Center *Sherlock // *web <https://www.sherlock.stanford.edu> | docs <https://www.sherlock.stanford.edu/docs> | status <https://status.sherlock.stanford.edu> | news <https://news.sherlock.stanford.edu>47733:1231609

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Cryo-EM Facility Manager - Berkeley California
by Paul Adams 18 May '21

18 May '21

Dear Colleagues, I would like to draw your attention to a job opening here in Berkeley California, for a Cryo-EM Facility Manager: https://lbl.referrals.selectminds.com/jobs/cryo-em-facility-manager-3801 This position requires expertise in biological cryo electron microscopy (cryo-EM). The successful candidate will be responsible for maintaining the in-house transmission electron microscopes (TEMs) and accessory equipment in excellent working order as well as training new users, scheduling access, and assisting with the collection of high-quality data. Duties will include providing complex technical support for sophisticated biotech-laboratory equipment including maintenance, calibration, repair and troubleshooting of instrumentation, control systems, experimental apparatuses, computers, and peripheral equipment as well as coordinating and scheduling vendor related maintenance and repairs. This is a full time, 3 year, term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Diversity, equity, and inclusion are core values at Berkeley Lab. Our excellence can only be fully realized by faculty, students, and staff who share our commitment to these values. Successful candidates for our faculty positions will demonstrate evidence of a commitment to advancing equity and inclusion. Lawrence Berkeley National Laboratory encourages applications from women, minorities, veterans, and other underrepresented groups presently considering scientific research careers. Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding development opportunities. Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Deadline today -- IUCr SARS-CoV-2 special symposia.
by Pearce, N.M. (Nick) 17 May '21

17 May '21

Dear BB, As you might be aware, there are a few microsymposia that have been added to this year’s IUCr conference on developments around SARS-CoV-2. Given the wide interests of this board, I wanted to advertise all four of the sessions, for which the (official) deadline is TODAY: - Structural biology of coronaviruses This session covers new structural and functional insights about the life cycle and virus-host interaction of SARS-CoV-2 and other coronaviruses with a particular view to integrative uses of crystallography in connection with other methods. - New methods to fight the pandemic This session covers new methods in crystallography and structural biology to better understand SARS-CoV-2 and the COVID-19 pandemic, including advances in computational methods, beamline instrumentation and integrative structural biology. - Crystallography against Corona This session covers the efforts of the crystallographic community to find drug candidates for COVID-19 both in-silico and in the lab by using structural models of viral proteins. - Using crystallography for education during the pandemic Using crystallography for education during the pandemic *** Please submit your abstracts today! If this isn’t possible, email us to let us know you intend to submit an abstract in the coming days! *** For each session, 4 relevant abstracts will be selected for 20-minute presentations. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Looking forward to reading the abstracts, Session co-chairs

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questions about using experimental phases in phenix.refine
by David A Case 15 May '21

15 May '21

I'm trying to use experimental phases derived from an cryoEM density map do carry out reciprocal space refinement in phenix.refine. I used phenix.map_box to get the map coefficients, and then the CCP4 program chltofom (with the -colin-phifom flag) to create the HL coefficients from F/PHI computed from the electron density map. 1. If I ask for the mlhl target, I get quite odd target values, e.g. for a 2.9 Å data set: | normalized target function (mlhl) (work): -5862.311069 | | target function (mlhl) not normalized (work): -6438670043.811632 and attempted refinements more or less destroy my protein and increases both the mlhl target value and the R-factors. Is there an example data set I could access to help me find out what I'm doing wrong? (Using the ml target, as suggested in DeMaio et al, Nature Methods 10:1102, 2013, seems to work well, and has a postive target function, but seems sub-optimal if phase information is available.) 2. Is there a way to do a "simple" least-squares refinement, minimizing sum( w_i * |Fobs_i - Fcalc_i|**2 ) where both Fobs and Fcalc are treated as vectors? Does the ls target perhaps do this if use_experimental_phases=True? Usual apologies if there is some great tutorial on this that I've not found. ...thanks...dave case

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Release of ISOLDE 1.2
by Tristan Croll 13 May '21

13 May '21

Hi all, I'm very happy to announce the release of ISOLDE 1.2, now available for installation into the ChimeraX 1.2 release. To get it, first download and install ChimeraX 1.2 from https://www.rbvi.ucsf.edu/chimerax/download.html, then go to "Tools/More Tools..." in the menu and follow the links to install ISOLDE. Key new features include: * The ability to add residues to the ends of protein chains (see https://twitter.com/CrollTristan/status/1391747032579289089?s=20; support for nucleic acid chain extension still in development) * Lower-fidelity simulation modes for greatly improved performance on lower-end GPUs (see https://twitter.com/CrollTristan/status/1390709520876331009?s=20) * Commands to write input files for phenix.refine and phenix.real_space_refine with recommended settings for refining models from ISOLDE * Command to write a ProSMART-like restraint definition file to softly restrain the model to its current geometry in Refmac * Improvements to stability and performance of bulk solvent/scaling in crystallographic datasets * Short aliases for commonly-used commands to make life easier for power users. Please enjoy! Best regards, Tristan

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Scientific software programmer at UCLA
by Johan Hattne 12 May '21

12 May '21

Dear all; The Gonen lab at UCLA's Department of Biological Chemistry is looking for a research specialist in scientific software programming to develop software for computational biological image analysis. The Gonen lab works toward understanding how membrane proteins help cells maintain homeostasis. To that end, the lab studies channels, transporters, and receptors, structurally and functionally. More information about the lab can be found by visiting https://cryoem.ucla.edu/. Details about the position and application instructions here: https://hhmi.wd1.myworkdayjobs.com/External/job/University-of-California-Lo… // Best wishes; Johan

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Help with den refine
by Alex Singer 11 May '21

11 May '21

Hi: I recently installed the Linux-64 version of phenix1.19.2-4158 and used the command line to run phenix.den_refine. The command was just Phenix.den_refine xxx_refine_25.pdb xxx_refine_25.mtz (xxx is just the name of the project, and is made up, but I did the same thing for two different projects) And then it ran for a while until it started the initial minimization before the den routine, ie coordinate minimization before annealing and then it crashed with the error message TypeError: %d format; a number is required, not Autotype I believe this is a python error, but is there something straight-forward that I can do about this so that den_refine can work? Thanks for your help Dr. Alex U. Singer

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