- 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 18 May '21

18 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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Call for abstracts: IUCR session on SARS-CoV-2 structural biology
by Andrea Thorn 11 May '21

11 May '21

Dear all, Gianluca Santoni and I are co-chairing a session at IUCr meeting 2021 entitled "Structural biology of coronaviruses" on the 16th of August. The subject of the session are 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. Abstract deadline has been extended to the 15th of may. We will select 4 abstracts for a 20 minutes talk. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Please feel free to forward this to scientists who may want to contribute an abstract, including junior researchers! We are looking forward to the meeting and the abstracts, best wishes, Gian and Andrea -- Dr. Andrea Thorn | group leader andrea.thorn(a)uni-hamburg.de HARBOR (Institute for Nanostructure and Solid State Physics), Universität Hamburg Luruper Chaussee 149 / Bldg. 610 | 22761 Hamburg | Germany Tel. +49 (0)40 42838 3651 www.thorn-lab.de | www.insidecorona.de

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Re: [phenixbb] real space rotamer restrains
by Pavel Afonine 10 May '21

10 May '21

Dear Leonid, thanks for sharing this and for your patience while waiting for the fix! All the best! Pavel On 5/10/21 06:36, Leonid Sazanov wrote: > Dear Pavel, > > Many thanks for this fix! > > Using local_grid_search now does not produce those rare outliers - > illustrated in the attachment for the benefit of others. > > "Before" is the earlier version refine run and "after" is using > phenix/1.20-dev-4224. > > Best wishes, > > Leonid > > > On 27.04.21 01:46, Pavel Afonine wrote: >> Dear Leonid, >> >> this is fixed now, residues won't leave good density any more. Next >> nightly build (dev-4218): >> >> http://phenix-online.org/download/nightly_builds.cgi?show_all=1 >> >> should have the fix. >> >> Please note, this is not the official released version meaning that >> while it is automatically tested it is not tested as thoroughly as >> regular official releases. With this in mind, it is advisable to keep >> around whatever version you are using currently just in case while >> using the latest nightly! >> >> Let us know should you discover any more problems! >> >> Cheers, >> Pavel >> >> >> On 4/26/21 13:53, Pavel Afonine wrote: >>> Dear Leonid, >>> >>> thanks for sharing files and my apologies for slow replies. >>> >>> I was able to reproduce the issue and I'm on it investigating right >>> now. I agree, this looks bad! >>> >>> More soon as progress happens. >>> >>> All the best! >>> Pavel >>> >>>

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Call for abstracts: IUCR session on SARS-CoV-2 structural biology
by Gianluca SANTONI 10 May '21

10 May '21

Dear all, Andrea Thorn and I are co-chairing a session at IUCr meeting 2021 entitled "Structural biology of coronaviruses" on the 16th of August. The subject of the session are 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. Abstract deadline has been extended to the 15th of may. We will select 4 abstracts for a 20 minutes talk. You can submit your abstracts through the conference website: https://iucr25.org/scientific/ Please feel free to forward this to scientists who may want to contribute an abstract, including junior researchers! We are looking forward to the meeting and the abstracts, best wishes, Gian and Andrea

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Re: [phenixbb] quick demo of phenix.autosol ?
by James Holton 06 May '21

06 May '21

Thank you all for the excellent suggestions! I think the built-in tutorials are a good place to start. I noticed a couple of things: 1) the autosol GUI "Status" tab always shows the number of sites to be zero, despite having solved the structure. Is that a bug? 2) the autosol GUI requires data filenames to be non-unique after removing the directory names. These days a rather large fraction of data files are called "XDS_ASCII.HKL". Now, for me personally, I don't mind opening a shell and making some links, but the students are sometimes confounded by that. Am I not doing the workflow right here? Again, thank you all for all the effort that goes into making Phenix great! -James Holton MAD Scientist

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Phenix GUI showing unreadable squares
by Dong-Hua Chen 05 May '21

05 May '21

Hi All, I am trying to install Phenix version 1.19.2-4158 on a node of a cluster and the installation was complete. After I tried to run phenix, the pop-up window showed lots of unrecognized small squares instead of letters (see the picture attached). I also tried to install the version 1.18.2 and got the same problem. Any suggestions would be greatly appreciated. Thanks, Dong-Hua

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Postdoc position micro electron diffraction / single particle analysis @Braunschweig/Germany
by Blankenfeldt, Wulf 04 May '21

04 May '21

Dear colleagues, together with Rolf Müller (one of this year's Leibniz Prize winners in Germany) we are currently looking for a postdoc to help us establish micro electron diffraction (and single particle analysis) in natural product research. Details about the position can be found here: https://www.helmholtz-hzi.de/en/career/open-positions/jobs/view/job/details… I'd be grateful if you could inform potential candidates. Regards, Wulf ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Re: [phenixbb] Model required for combine_focused_maps
by Tom Terwilliger 03 May '21

03 May '21

Hi Fengwei, The model has to be pretty good as it is used to evaluate the maps. I would improve the model first, at least by refinement , then combine the maps, then maybe iterate the whole process with a new model. -Tom T On Mon, May 3, 2021 at 14:19 Zheng, Fengwei <Fengwei.Zheng(a)vai.org> wrote: > Dear Phenix developers: > > Thank you for developing this so powerful and elegant software packages > for our community! > > I am a newbie in cryoEM, and recently I got a consensus map, and split it > into two parts to do the further focused refinement, after that I want to > combine them together, and then to build my model, I learned that this > "combine focused maps" module in Phenix can achieve this, I read through > this online tutorial ( > https://www.phenix-online.org/documentation/reference/combine_focused_maps.…), > for the starting input files, I seem need to provide my initial/consensus > map, two focused maps and a model, but I have a question about this > provided model: > > 1st, need me to provide my final refined model (i.e. I need to finish my > model building firstly according to my two focused maps), or I can use a > homologue model for this combination? > > 2nd, if I use a homologue model that only can be roughly fitted into my > consensus map, will this affect my final combination results? > > Appreciate! > > Best, > Fengwei > > -- 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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Error at fix_insertions_deletions
by Carlos HENRIQUE FERNANDES 03 May '21

03 May '21

Hello all! I'am facing a problem running the phenix.fix_insertions_deletions. I'am using in the command line: phenix.fix_insertions_deletions sharpened_map.ccp4 resolution=3.5 protein.pdb seq.dat I've been encountering this error: File "/usr/local/phenix-1.19.2-4158/build/../modules/phenix/phenix/command_line/fix_insertions_deletions.py", line 7, in <module> run_program(program_class=fix_insertions_deletions.Program) File "/usr/local/phenix-1.19.2-4158/modules/cctbx_project/iotbx/cli_parser.py", line 72, in run_program task.run() File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/programs/fix_insertions_deletions.py", line 515, in run self.fix_insertions_deletions.run() File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1331, in run self.run_macro_cycles() File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1464, in run_macro_cycles self.run_cycles(mc=mc) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1485, in run_cycles self.overall_rebuild_worst_residues(icycle,mc=mc) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1528, in overall_rebuild_worst_residues mc=mc) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 1027, in rebuild_worst_residues map_coeffs=map_coeffs) File "/usr/local/phenix-1.19.2-4158/modules/phenix/phenix/autosol/fix_insertions_deletions.py", line 589, in rebuild_one_loop end_rebuild=end_rebuild,) UnboundLocalError: local variable 'new_model' referenced before assignment Has anyone encountered this error before? Thanks in advance, Carlos Fernandes

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quick demo of phenix.autosol ?
by James Holton 02 May '21

02 May '21

Hello all, I'm involved in an X-ray course at Stanford this coming week and one of the things we want to do is demonstrate things like phenix.autosol. However, typical run times with borderline data and default settings can be more than a few minutes. Can anyone recommend a test data set / settings where phenix.autosol finishes very quickly? I was going to try and whip something up that is small, moderate resolution, screaming phasing signal, etc. However, since I'm sure many on this mailing list have done this hundreds of times you no doubt have a favorite example off the top of your head? thanks again! -James Holton MAD Scientist

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Refinement of a b-Strand swapped into the sheet of the symmetry related copy
by Matthias Uthoff 28 Apr '21

28 Apr '21

Hi phenixbb, I am working on a homodimer. Each protein has an internal b-sheet with three b-strands, however the sheets swap their middle strands. So a sheet consists of one strand from molecule A surrounded by two strands from molecule B or vice versa. As I am at 3 A resolution, I would like to set secondary structure restraints including correct hydrogen bonding between the strands of the two molecules. My problem: There is only one protein in the ASU and the "other" molecule is in deed just a symmetry mate. Phenix is not able to automatically detect this and if I provide the restraints myself, phenix discards them as it is falsely assuming the b-sheet is intramolecularly (all on chain A) and hence the strands are 30ish A apart. What is the best way of refining this feature? Thanks in advance, Matthias -- Matthias Uthoff, PhD Student University of Cologne Institute for Biochemistry Zülpicher Straße 47 D-50674 Cologne Phone: +49 221 470 3211 E-Mail:[email protected] Internet:http://px.uni-koeln.de

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Online Course on Neutron Scattering Applications in Structural Biology (HANDS2021)
by Meilleur, Flora 27 Apr '21

27 Apr '21

ORNL Online Course on Neutron Scattering Applications in Structural Biology: https://conference.sns.gov/event/291/ Lectures: June 21 - June 25, 2021 Tutorials: June 28 - 30, 2021 2:00 pm - 5:30 pm EST Registration (free) is now open and will close May 14, 2021: https://conference.sns.gov/event/291/registrations/ 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. Lectures will cover basic concepts, sample preparation, instrumentation and applications. Data collection and processing will be discussed in tutorials.

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temp files
by James Holton 26 Apr '21

26 Apr '21

Hello all, Is there a way to configure phenix at install time (or perhaps post-install) to put temporary files under /tmp ? I just had to delete 20e6 temp files over NFS from a single user's phenix ligand identification run. The delete took almost a month. Apologies if I am neglecting to look somewhere obvious in the documentation, Happy Weekend! -James Holton MAD Scientist

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Job posting: Scientist-I (Structural biology) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 21 Apr '21

21 Apr '21

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology (crystallography). The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-protein and protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leido… Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research 8560 Progress Drive, C1012, Frederick, MD 21701 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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Caltech Postdoc Position
by Hoelz, Andre 19 Apr '21

19 Apr '21

The Hoelz laboratory at the California Institute of Technology seeks to recruit two outstanding postdoctoral scientists in structural cell biology. Our laboratory focuses on the structure-function relationships of the nuclear pore complex and associated nucleocytoplasmic transport machinery. This position requires a recent Ph.D. degree in biochemistry/biophysics with a strong background in biochemistry, x-ray crystallography, and/or cryo-electron microscopy/tomography. The successful applicant should be a highly motivated individual with good organizational, communication, and interpersonal skills, who is able to carry out a structure determination project from the development of recombinant protein expression systems to structure refinement. The laboratory is well-funded and equipped with modern biophysical instrumentation. Importantly, Caltech has an exceptional infrastructure for structural biology, including access to a high intensity, completely automated, state-of-the-art crystallography beamline at the Stanford Synchrotron Radiation Lightsource (SSRL), as well as an excellent cryo-electron microscopy facility with access to FEI Arctica and Titan Krios microscopes equipped with Gatan K3 cameras. The positions are available immediately and funded for 3+ years. Depending on performance, the position can be extended for additional years. To apply, please send your CV, a statement of research interests, and the names and contact information of at least two references to André Hoelz (hoelz(a)caltech.edu<mailto:[email protected]>). Selected Publications Lin, D. H., Hoelz, A.* (2019). The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725-783. Lin, D. H., Correia, A.C., Cai, S.W., Huber, F.M. Jette, C.A., Hoelz, A.* (2018). Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat. Commun., 2319. Huber, F., Hoelz, A.,* (2017). Molecular basis for protection of ribosomal protein L4 from cellular degradation, Nat. Commun. 8, 14354. Lin, D.,# Stuwe, T.,# Schilbach, S., Rundlet, E.J., Perriches, T., Mobbs, G., Fan, Y., Thierbach, K., Huber, F.M., Collins, L.N., Davenport, A.M., Jeon, Y.E., Hoelz, A.* (2016). Architecture of the symmetric core of the nuclear pore, Science 352, aaf1015. [Cover] Stuwe, T.,# Bley, C.J.,# Thierbach, K.,# Petrovic, S.,# Schilbach, S., Mayo, D.J., Perriches, T., Rundlet, E.J., Jeon, Y.J., Collins, L.N., Huber, F.M., Lin, D.H., Paduch, M., Koide, A., Lu, V., Fischer, J., Hurt, E., Koide, S., Kossiakoff, A., Hoelz, A.* (2015). Architecture of the fungal nuclear pore inner ring complex, Science 350, 56-64. Stuwe, T.,# Correia, A.,# Lin, D. H., Paduch, M., Lu, V. T., Kossiakoff, A. A., Hoelz, A.* (2015). Architecture of the nuclear pore complex coat. Science 347, 1148-1152. Hoelz, A.,* Debler, E.W., Blobel, G. (2011). Structure of the Nuclear Pore Complex, Annu. Rev. Biochem. 80, 613-643. --- André Hoelz, Ph.D. Faculty Scholar, Howard Hughes Medical Institute Investigator, Heritage Medical Research Institute Professor of Chemistry and Biochemistry Division of Chemistry and Chemical Engineering California Institute of Technology <x-apple-data-detectors://2><x-apple-data-detectors://2>1200 East California Boulevard<x-apple-data-detectors://2> Pasadena, CA 91125<x-apple-data-detectors://2> <x-apple-data-detectors://2><x-apple-data-detectors://2>U.S.A.<x-apple-data-detectors://2> Tel: 1-626-395-8480<tel:1-626-395-8480> (office) Tel: 1-626-395-3152<tel:1-626-395-3152> (lab) http://ahweb.caltech.edu<http://ahweb.caltech.edu/>

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UnicodeEncodeError in Windows 10 Edu
by ‍김현우[ 학부졸업 / 생명과학부 ] 13 Apr '21

13 Apr '21

Hi everyone. I've installed open source pymol, coot, and phenix on my Windows 10 laptop. Pymol, python, and coot works fine, but when I launched phenix, it didn't work I tried both 1.18 and 1.19 version point-and-click installers. So I executed phenix on cmd, and the following error occured: ****************************************************************************** C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\build\bin>phenix Traceback (most recent call last): File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\build\..\modules\phenix\wxgui2\command_line\main.py", line 23, in <module> run(sys.argv[1:]) File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\build\..\modules\phenix\wxgui2\command_line\main.py", line 17, in run wxapp = App.PhenixApp(args) File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\modules\phenix\wxGUI2\App.py", line 70, in __init__ wx.App.__init__(self, 0) File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\conda_base\lib\site-packages\wx-3.0-msw\wx\_core.py", line 8628, in __init__ self._BootstrapApp() File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\conda_base\lib\site-packages\wx-3.0-msw\wx\_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\modules\phenix\wxGUI2\App.py", line 90, in OnInit self.setup_user_dir() File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\modules\phenix\wxGUI2\App.py", line 364, in setup_user_dir os.environ['PHENIX_DATA'] = wxGUI2.PHENIX_USER_DIR File "C:\Program Files\Phenix\phenix-installer-1.18.2-3874-intel-windows-x86_64\conda_base\lib\os.py", line 422, in __setitem__ putenv(key, item) *UnicodeEncodeError: 'ascii' codec can't encode characters in position 9-11: ordinal not in range(128)* ****************************************************************************** I found out that unicode errors occur frequently and are easy to fix, but I can't figure out which file and which line I should manipulate. I'd appreciate any reply on this matter. Hyunwoo Kim

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Please register - Phenix Workshop - April 14
by Paul Adams 08 Apr '21

08 Apr '21

Dear Colleagues, The Phenix developers will be holding another online *Phenix User Workshop on the 14th of April at 4-9pm PDT.* These times will work best for researchers in Asia and Australasia. The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. The workshop will cover aspects of macromolecular crystallography in Phenix, with the final emphasis based on the applicants’ research interests. To apply please fill out this form <https://forms.gle/X18KrWR6GvRUKYJ49>. We will make every effort to accommodate all applicants, but may need to defer some requests to a future workshop if demand is high. We are hoping this workshop will be a success, in which case we plan to host more in the future. *AGENDA:* *14 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Pavel Afonine - Real Space Refine - 5.15pm - Nigel Moriarty - Ligands and Restraints - 6.00pm - Jane Richardson - Validation - 7.00pm - Question/Answer session The recorded workshops are here <https://www.youtube.com/c/PhenixTutorials/playlists> for these and previous ones. Cheers, The Phenix Developer Team -- 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) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley ( http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ AshleyDawn(a)lbl.gov <LBenvenue(a)lbl.gov> ] [ 1-510-486-5455 ]

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Automated water building into high-resolution cryo-EM maps (phenix.douse)
by Pavel Afonine 05 Apr '21

05 Apr '21

To all who reported multiple bugs and performance issues in phenix.douse: Phenix version dev-4196 and later now has all previously reported bugs and performance issues (slowness and memory consumption) fixed: http://phenix-online.org/download/nightly_builds.cgi?show_all=1 Please let us know should you find any more problems or have feature suggestions. phenix.douse is a tool to build water into high-resolution cryo-EM maps automatically. Background and details can be found here: http://phenix-online.org/presentations/water.pdf All the best! Pavel

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Fwd: Thank you for registering - Phenix Workshops - April 7 & 14
by Nigel Moriarty 05 Apr '21

05 Apr '21

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 ORCID : orcid.org/0000-0001-8857-9464 ---------- Forwarded message --------- From: Ashley Dawn <ashleydawn(a)lbl.gov> Date: Mon, Apr 5, 2021 at 9:56 AM Subject: Thank you for registering - Phenix Workshops - April 7 & 14 To: Ashley Dawn <ashleydawn(a)lbl.gov> Cc: Nigel Moriarty <nwmoriarty(a)lbl.gov>, Christopher Schlicksup < cjschlicksup(a)lbl.gov>, phenixdev <developers(a)phenix-online.org> Good morning, Thank you for registering for the Phenix Workshops that begin this Wednesday. *AGENDA: * *7 APR *(click to add to google calendar) <https://calendar.google.com/event?action=TEMPLATE&tmeid=MHRzaGc4ZDR0MDVpcjd…> - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Paul Adams - Phenix Overview - 4.30pm - Tom Terwilliger - Map Improvement - 5.45pm - Tom Terwilliger - Model Building - 7.00pm - Question/Answer session *14 APR * (click to add to google calendar) <https://calendar.google.com/event?action=TEMPLATE&tmeid=NXBhcmkxcTYzdmp1ZGN…> - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Pavel Afonine - Real Space Refine - 5.15pm - Nigel Moriarty - Ligands and Restraints - 6.00pm - Jane Richardson - Validation - 7.00pm - Question/Answer session Cheers, The Phenix Developer Team Ashley Dawn (she/her/hers) [image: A button for name playback in email signature] <https://www.name-coach.com/ashley-dawn> Senior Administrator Molecular Biophysics & Integrated Bioimaging Lawrence Berkeley Laboratory 1-510-486-5455

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Please register - Phenix Workshops - April 7 & 14
by Paul Adams 05 Apr '21

05 Apr '21

Dear Colleagues, The Phenix developers will be holding an online *Phenix User Workshop on the 7th and 14th of April at 4-9pm PDT.* These times will work best for researchers in Asia and Australasia. The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. The workshop will cover aspects of macromolecular crystallography in Phenix, with the final emphasis based on the applicants’ research interests. To apply please fill out this form <https://forms.gle/X18KrWR6GvRUKYJ49>. We will make every effort to accommodate all applicants, but may need to defer some requests to a future workshop if demand is high. We are hoping this workshop will be a success, in which case we plan to host more in the future. *AGENDA:* *7 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Paul Adams - Phenix Overview - 4.30pm - Tom Terwilliger - Map Improvement - 5.45pm - Tom Terwilliger - Model Building - 7.00pm - Question/Answer session *14 APR * - 3.45pm - Start of Zoom session (for people to debug any issues) - 4.00pm - Pavel Afonine - Real Space Refine - 5.15pm - Nigel Moriarty - Ligands and Restraints - 6.00pm - Jane Richardson - Validation - 7.00pm - Question/Answer session Cheers, The Phenix Developer Team -- 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) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley ( http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ AshleyDawn(a)lbl.gov <LBenvenue(a)lbl.gov> ] [ 1-510-486-5455 ]

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phenix.ligand_identification search_center
by Tanner, John J. 31 Mar '21

31 Mar '21

Phenix BB: I would like to use phenix.ligand_identification to analyze an electron density feature in the active site of an enzyme; however, I do not see how to specify search_center in the gui. Thus, the program places the ligands into a strong density feature on the surface of the protein. When I run it from the command line with search_center specified, it seems to ignore the search center coordinates and again places the ligands into the density feature on the surface. My command script: [tannerjj@europa ligandID]$ cat ligandID.com phenix.ligand_identification \ mtz_in = "/titan/tanner/MmP5CDH/THLP/MmALDH4A1_THLP8-1_003.mtz" \ mtz_type = diffmap \ input_labels = "FOFCWT PHFOFCWT" \ ligand_list = "DPR PRO HYP HZP UYA UY7" \ model = "/titan/tanner/MmP5CDH/THLP/MmALDH4A1_THLP8-1_003.pdb" \ ncpu = 4 \ output_dir = "/titan/tanner/MmP5CDH/THLP/ligandID/temp" \ number_of_ligands = 6 \ job_title = "THLP8-1_003 D,L-Pro and 4 OH-Pro stereoisomers" \ search_center = "-12.597 11.990 21.741" [tannerjj@europa ligandID]$ Thanks, Jack -- John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj(a)missouri.edu<mailto:[email protected]> https://cafnrfaculty.missouri.edu/tannerlab/ Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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phenix.local_aniso_sharpen
by Luca Pellegrini 31 Mar '21

31 Mar '21

Hi, Is there a way to estimate the resolution of the map obtained from phenix.local_aniso_sharpen? I find that it produces nice maps, but there’s no output information that I can see. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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cif. file for AFITT
by Muhammad Bashir Khan 26 Mar '21

26 Mar '21

Hello all Could somebody explain how I can generate a cif. file of ligand for AFITT. I am using afitt in phenix refinement using the ligand cif. file generated by the elbow. But it complains. I have two different types of ligands in the structure. Thanks Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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Unusual ligand conformation
by Joel Tyndall 26 Mar '21

26 Mar '21

Hi all, We have been finalising a structure with a ligand complexed to heme. I have been checking the close to final structure and I noticed that the ligand looks distorted away from what one would expect. We use Phenix.refine We initially used the grade server for our restraints files. I also just used elbow to generate a new one. Looking at both, the restraints look reasonable (similar in both) however the initial output pdb from elbow is distorted further. The angles /lengths looked reasonable and are similar to small molecule structures (CCDC). The planarity of a bi-phenyl moiety is very distorted. [cid:[email protected]] Are we missing something? Do we need to tell phenix.refine to not over refine the model? Should elbow give a distorted model? Apologies if this is all online but my uni cant seem to access phenix.org! Thanks in advance Joel Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Skype: jtyndall Website | pharmacy.otago.ac.nz

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map to model FSC calculation
by C.J. 23 Mar '21

23 Mar '21

Hi All, I'm new to phenix and a bit confused to map to model FSC calculation. Which program should I use, phenix.mtriage or phenix.map_model_cc? If both work, what is the difference between them? Thank you! Jianhao

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Re: [phenixbb] FSC curves
by Pavel Afonine 19 Mar '21

19 Mar '21

Hi Juliana, > After running phenix real space refine with different refinement > strategies. My map-model FSC curve has some interesting features: > > 1. It does not starts at 1 as it does the map FSC curve, is that ok? > What could be causing this? > which one is it? Is it FSC(half_map1, half_map2) or FSC(experimental_map, model_map) ? > 1. It has a dip around 5-6Å, this deep can be a bit up or down > depending the refinement strategy I use, therefore the FSC model > at 0.5 can cut the resolution at 3.9 or 6 Å. What this deep mean? > Am I doing something wrong in the refinement? > How different these models are? > 1. The mask and unmask curves completely overlap, is that ok? > This suggests to me the map is probably already masked or somehow 'normalized'.. > 1. Also, my refinement shows a high clash score (15-20), if I change > the nonbonded_weight parameter from 100 (default) to higher values > the clash score decreases but the FSC curves gets lower them the > FSC curve crosses the 0.5 cutoff at 6A. > When it comes to clashscore, generally the lower the better but zero is not the goal. Looking at one of screenshots I see you have 2.42% of atoms with occupancy less than 1. Do you really see partially occupied atoms in 4A resolution map? Unlikely! So.. please check those out! I can run more diagnostics for you if you share maps and models (off-list of course!). Pavel

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on "Tutorial: Solving a structure with cryo-EM data using docking"
by Smith Lee 19 Mar '21

19 Mar '21

Dear All, For "Tutorial: Solving a structure with cryo-EM data using docking", it is easy to download the emd_20026_half_map_1_box.ccp4 and emd_20026_half_map_2_box.ccp4 from the emd-20026 depositation, but will you please let me know step by step how to get the tutorial used seq.dat, 20026_auto_sharpen_A.ccp4 (any other name for this file? Cannot find the exact name file in emd_20026 depositation), apoferritin_chainA_rsr.pdb (it mentioned "model refined against sharpened map", which sharpened map, and what was the refinement method ued?), run_denmod_dock.csh? I am looking forward to getting your reply. Best wishes, Smith

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Ligand refinment problum
by Muhammad Bashir Khan 18 Mar '21

18 Mar '21

Hello all; I have a crystal structure with four molecules per unit of the cell. It contains two different ligands. Four are similar while the fifth one is different. Placed all the five ligands manually by coot. Now I want to refine. Before refinement, I run the ReadySet to generate the cif. file. It shows an error. Then I supply the cif. file of both the ligand coming from the elbow, It still shows the following error. screenshot attached. Any help would be appreciated. Sincerely; Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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rotamers in real space refine
by Leonid Sazanov 17 Mar '21

17 Mar '21

Hi, We still have a problem of some Trp and Tyr residues going out of very clear density in high-resolution (~2.5 A) EM maps upon real space refine in phenix, even the latest version. Is there may be a more extensive rotamer library (including those pseudo-"outliers") available somewhere to be used in Phenix? Many thanks, Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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Migrating all phenix projects to a new location without breaking all of the file paths.
by Leonard,Paul G 15 Mar '21

15 Mar '21

Hi, Does anyone have instructions I can follow for how to move all of my phenix directories to a new location without messing up all of the file paths in each project. Our IT department wants to relocate files on our server which will change all of the top directory locations to something new so before that happens I think there is a way I can have a file that will allow me to recreate all of the phenix projects in the GUI with the new file paths but I can't recall how to do it. Thanks in advance for your assistance. Best wishes, Paul Institute Senior Research Scientist MD Anderson Cancer Center 1881 East Road Houston TX 77054 USA Tel: 732 397 8539 email: pleonard1(a)mdanderson.org The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Is the Phenix website down?
by Joel Tyndall 13 Mar '21

13 Mar '21

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Re: [phenixbb] Question about Phenix refinement
by Dorothee Liebschner 12 Mar '21

12 Mar '21

Hi, This tutorial explains how to set parameters: https://www.youtube.com/watch?v=qB8W_6yuw5k&t=2s Best wishes, Dorothee On Fri, Mar 12, 2021 at 7:39 AM Zhang, Wen <wz15(a)iu.edu> wrote: > Hi, > > This is Wen from Indiana University. I have a question about the > refinement using Phenix. I got a Phenix Error, saying “Polymer crosses > special position element xxxxxxxxx. Use > allow_polymer_cross_special_position=True to keep going.” I also find this > keyword online, but am still not sure how I can change this key word. > Should I input the command somewhere? What should I do exactly? > > > > Thanks > > Wen > -- 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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Adding hydrogens back on lipids
by Noor Agip 11 Mar '21

11 Mar '21

Hi, Is there a way to add hydrogens back on lipids using Readyset? I tried this with no success. Best wishes, Noor

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Refining ligands in a structure
by Joel Tyndall 11 Mar '21

11 Mar '21

Hi folks, It has been a while since we have done much with phenix. We are refining a structure with a known ligand, voriconazole (exists on the pdb). We get an error regarding a lack of .cif file/restraints. Do we normally need to specify a cif file given this is a known ligand and can be retrieved in Coot? I assume that phenix would call on a known library of ligands/monomers that are known. Is this the correct library? phenix-installer-1.17.1-3660-intel-windows-x86_64\modules\chem_data\chemical_components\ Many thanks Joel Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Skype: jtyndall Website | pharmacy.otago.ac.nz

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Postdoctoral position in drug discovery at Vanderbilt University (Nashville, TN)
by Harp, Joel M 08 Mar '21

08 Mar '21

Postdoctoral position in drug discovery An opening is available in the drug discovery laboratory of Dr. Stephen Fesik for a post-doc in the field of protein x-ray crystallography. Responsibilities will include protein expression and purification, and all aspects of x-ray crystallography including preparation of protein-inhibitor complexes, crystallization, home/synchrotron data collection, and structure determination. Additional experiences in molecular biology including construct design, cloning, site-directed mutagenesis, and experience with recombinant protein expression in eukaryotic cells are highly preferred. The ideal candidate should be self-motivated and be able to communicate efficiently in a highly collaborative environment. Please send cv to jason.phan(a)Vanderbilt.Edu<mailto:[email protected]>

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Spatial query acceleration structure in cctbx?
by Russell M. Taylor II 08 Mar '21

08 Mar '21

As part of integrating the MolProbity tools more tightly with the CCTBX, I'm modifying the Probe code that will be shared by it and Reduce to use native CCTBX structures. One of the structures is a spatial map to accelerate the search for nearby atoms in a model. Before building my own (3D grid with near neighbors listed, ability to insert and remove atoms as they move), I wanted to check and see what was already available in the CCTBX. I looked at the page listing the CCTBX core objects and functions and did not see one, and searching for "spatial" and "accel" in the source tree did not turn up anything promising. Is there one already in there? If not, is this something that others would find to be a useful tool and, if so, where should it live? Otherwise, I'll make it part of Probe. Thanks, Russ Taylor --- Russell M. Taylor II, Ph.D. russ(a)reliasolve.com taylor(a)redbudlabs.com rtaylor(a)aqueti.com russ(a)outloveracism.org www.cs.unc.edu/~taylorr

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PAIREF Webinar (23rd March 2021, 15:00 CET)
by Petr Kolenko 08 Mar '21

08 Mar '21

Dear colleagues, We are pleased to announce the webinar on paired refinement to be held on March 23, 2021, from 3 PM (CET) to 4 PM (CET). This protocol provides an accurate estimation of the high-resolution cutoff (https://journals.iucr.org/m/issues/2020/04/00/mf5044/). The "PAIREF webinar" will be a free virtual event for up to 300 participants. The meeting will be recorded. Please register and receive your Zoom link here: https://kipl-indico.fjfi.cvut.cz/e/pairef We will cover: 1. Introduction to paired refinement. 2. Installation of PAIREF for CCP4 and/or PHENIX users. 3. Short tutorial (files will be provided). 4. Discussion. Feel free to contact us with your data. Best regards, Petr Kolenko, Martin Maly, Kay Diederichs and Jan Dohnalek

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error for "rosetta.run_tests"
by Smith Lee 06 Mar '21

06 Mar '21

Dear All, For rosetta installation for use in phenix, in the .bashrc I have: export PATH="/home/usrname/rosetta_src_2020.08.61146_bundle":$PATHexport PATH="/home/username/phenix11914122installdir/phenix-1.19.1-4122/build/bin":$PATH and I have the .bashrc file sourced. However when I run "rosetta.run_tests", I got the following error: --...... End of input processing Sorry: The RosettaScripts executable could not be located. Please set the environmental variable PHENIX_ROSETTA_PATH or add the appropriate directory to your PATH environment variable. ---- I am looking forward to getting your advice on how to solve the error issue. Smith

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phenix.molprobity geo
by Paul Emsley 04 Mar '21

04 Mar '21

Hello, I'd like to compare the restraints generated by Coot to the validation provided by molprobity. When I run phenix.molprobity on my model, it gives me (amongst other things) this: ----------------------- Histogram of nonbonded interaction distances: 1.87 - 2.42: 526 2.42 - 2.96: 3217 2.96 - 3.51: 3639 3.51 - 4.05: 5026 4.05 - 4.60: 6847 Nonbonded interactions: 19255 Sorted by model distance: nonbonded pdb=" O LEU A 21 " pdb=" H GLY A 26 " model vdw 1.874 1.850 nonbonded pdb=" H ILE A 71 " pdb=" O TYR A 80 " model vdw 1.920 1.850 nonbonded pdb=" H GLY A 34 " pdb=" O GLU A 54 " model vdw 1.925 1.850 nonbonded pdb=" O ILE A 71 " pdb=" H TYR A 80 " model vdw 1.937 1.850 nonbonded pdb=" HE ARG A 40 " pdb=" HG1 THR A 76 " model vdw sym.op. 1.955 2.100 -x+3/2,-y,z+1/2 ... (remaining 19250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. -------------------------- I don't understand this lilst. Should I be concerned by those interactions? Which of these atom pairs are contributing to the clashscore? Perhaps the details are in the .geo file? How do I get a .geo file? I googled, I didn't find the answer. How could I have found the answer without asking here? Thanks, Paul.

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Re: [phenixbb] executing Phenix in a python script on a Windows OS
by Muriel Gelin 02 Mar '21

02 Mar '21

Here is what I have: In a prompt: C:\Users\MG>C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat C:\Users\MG>phenix.refine Usage: phenix.refine [options] [reflection_file] [pdb_file] [parameter_file] -------------------------------------------------------------------------------- In python: source = subprocess.Popen(str(r"C:\Users\MG\Phenix\phenix-installer-1.19.1-4122-intel-windows-x86_64\phenix_env.bat"), stdin=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) >>> phenix.refine Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'phenix' is not defined >>> py phenix.refine File "<stdin>", line 1 py phenix.refine ^ -------------------------------------------------------------------------------- If somebody see what is the problem. I'm afraid I am stuck ... Thank you all. Muriel Le 02/03/2021 à 11:03, gelin a écrit : > Dear Bernhard, > > Thank you for your answer. > > Executing phenix_env.bat in Windows command prompt works well, since I > can then execute phenix.refine in the prompt. > > So I tried to add in my python script something like that: > source = subprocess.Popen(my_path\phenix_env.bat, > stdin=subprocess.PIPE, stdout=subprocess.PIPE, > stderr=subprocess.PIPE) > Unfortunately, it doesn't work. I suppose the prompt environment is > not modified. > > Do you know how to do that in my python script so that I can then > execute something like: > xtriage = subprocess.Popen(["phenix.xtriage", my_mtz, > "parameters.reporting.log=" + "xtriage.log")], > stdin=subprocess.PIPE, > stdout=subprocess.PIPE, stderr=subprocess.PIPE) > > Thank you for you help. > > Muriel > > Le 2021-03-01 18:36, Bernhard Rupp a écrit : >> Here is what I did: >> >> Install phenix >> >> make a batch command in your path (eg phx.bat) that executes the >> environment setup, eg. >> C:\Phenix\phenix-installer-1.19-4092-intel-windows-x86_64\phenix_env.bat >> >> Open terminal, execute that batch (modify as you like), and there you go >> >> c:\data\Dropbox\Refinements\5okl>phenix.refine >> Usage: phenix.refine [options] [reflection_file] [pdb_file] >> [parameter_file] >> .... >> >> Best, BR >> >> -----Original Message----- >> From: phenixbb-bounces(a)phenix-online.org >> <phenixbb-bounces(a)phenix-online.org> On Behalf Of Muriel Gelin >> Sent: Monday, March 1, 2021 09:08 >> To: phenixbb(a)phenix-online.org >> Subject: [phenixbb] executing Phenix in a python script on a Windows OS >> >> Dear Phenix community, >> >> I wrote a python script to automate the processing of our data with >> Phenix. I'm not a developer by profession, but a crystallographer, and >> write scripts usually under Linux. My colleagues working under Windows >> asked me to share my script. >> >> I managed to run a simple python script under windows, no problem. But >> for a script that executes Phenix, it's not so easy (for me). >> >> Under Linux, I manage to source phenix_env.csh, but under Windows what >> is the command to setup Phenix in order to simply use phenix.refine >> or phenix.xtriage in my script? >> >> All I can find is this page >> https://www.mrc-lmb.cam.ac.uk/public/xtal/doc/phenix/install-setup-run.html >> >> >> but I don't think it answers my question. >> >> Thank you in advance for your help! >> >> Muriel >> >> -- >> Dr Muriel Gelin >> >> Research Engineer >> Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced >> Biology, Chemistry, Informatics Studio" >> >> CNRS UMR 5048 - UM - INSERM U 1054 >> 29 rue de Navacelles >> 34090 MONTPELLIER Cedex - FRANCE >> http://www.cbs.cnrs.fr >> >> Tel: (33) 04 67 41 77 12 >> >> >> -- >> This message has been scanned for viruses and dangerous content by >> MailScanner, and is believed to be clean. >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > -- Dr Muriel Gelin Research Engineer Centre de biochimie Structurale de Montpellier Team "ABCIS: Avanced Biology, Chemistry, Informatics Studio" CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 12 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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on rosetta installation for phenix
by Smith Lee 02 Mar '21

02 Mar '21

Dear All, I have tried to install Rosetta for phenix use based on the guide in https://www.phenix-online.org/documentation/reference/rosetta_install.html. After the "tar xzf..." command, I added the directory for the installed rosetta (something like "export PHENIX_ROSETTA_PATH=/your-path-to-rosetta-here/") to my .bashrc (and in fact I also have added into /bash_profile) and sourced it. For the final step to build the interface for rosetta_refine, as for my gcc version is 8.3.1, I have deleted the original site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/, and exactly copied the content in https://www.phenix-online.org/documentation/extras/site.settings and save it as site.settings in the directory ${PHENIX_ROSETTA_PATH}/main/source/tools/build/. Command "nproc" displays 12, then I run "rosetta.build_phenix_interface nproc=12". In the running step for the above command, I remember it asked me "whether to install "sed" (I do not what is "sed" for), I answer "y" and "enter", it seems like the computer stopped. I opened another terminal, and all commands like "ls","cd" failed to work. I restarted the computer, but I cannot log into my centos username account anymore. I restarted the computer by initiating the centos secure start system, and deleted the export directory for the rosetta from the .bashrc and .bash_profile. In this way I restarted the computer and I can log into my centos user name account as usual. But as you know, my rosetta still did not work. Thus, will you please advice what is wrong for my installation fof the rosetta (for phenix use) and how to make it workable? I am looking forward to getting your reply. Best wishes, Smith

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