- phenixbb - phenix-online.org

cctbx now available on conda-forge
by Billy Poon 23 Sep '20

23 Sep '20

Hi everyone, The conda-forge package for cctbx is now available. There are 2 packages, "cctbx-base" includes the base code and "cctbx" which includes "cctbx-base" and adds "wxPython", "PySide2", and "ipython". The commands for installing cctbx into your conda environment are conda install -c conda-forge cctbx or conda install -c conda-forge cctbx-base If you want to use Jupyter Lab, you can now easily do this with conda install -c conda-forge cctbx-base jupyterlab jupyter lab The existing documentation will be updated to reflect the easier installation procedure with conda. After installing the conda package, you can also run some of the tests (in an empty directory) with libtbx.run_tests_module module=libtbx module=cctbx nproc=<nproc> I do know of a few issues that I want to fix in upcoming releases, but please submit issues to https://github.com/cctbx/cctbx_project with steps to reproduce the error. Thanks! -- 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

1 1

Issues with ligandfit.
by Vatsal Purohit 17 Sep '20

17 Sep '20

Hi, I’ve been using the Ligandfit function to location ligand binding sites using electron density obtained without any ligands in the structure model. However, recently, the program has been giving me the following error while trying to open the resolve maps: Sorry: None of the resolve versions worked Is there something I can do to try and fix this? Any advice would be appreciated. Regards, Vatsal Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

How to generate metal coordination restrain
by Shramana Chatterjee 17 Sep '20

17 Sep '20

Hi, I am trying to generate restraints for metal ions. Ready set is processing the pdb but it is not generating any output file. I don't want to add hydrogens to the model. Therefore readyset is generating only .edits file and finally I am unable to get any metal coordination restrains in Coot It would be very helpful if I get any suggestions about the above-mentioned problem. Thank you in advance. Regards, Shramana

3 2

Job Vacancy: Postdoctoral research fellow position available in Therapeutics Discovery Division at MD Anderson Cancer Center
by Leonard,Paul G 15 Sep '20

15 Sep '20

Hi, A postdoctoral position is currently available in the Structural Chemistry group, part of the Institute for Applied Cancer Science (IACS) within the Therapeutics Discovery Division of MD Anderson Cancer Center. Our mission is to integrate novel biological insights with drug discovery expertise to accelerate the development of innovative, targeted, small-molecule therapeutics for unmet medical needs. Our work is conducted in a team science environment that brings together excellence in both academic and pharmaceutical discovery, as evidenced by recent publications. We are seeking a highly motivated individual with a strong background in structural biology, including protein expression and purification, protein crystallization, and X-ray crystallography structure determination. Experience with cryo-EM structure determination and/or structure determination of membrane proteins is not required, but would be advantageous. We are seeking only the most dedicated individuals who will join us in our quest to discover, develop and deliver more effective treatments to our patients. This is a unique opportunity to participate in project-driven drug discovery research within a highly respected academic and clinical setting. Interested individuals should apply via the Postdoc Jobs website. https://www.postdocjobs.com/posting/7069370 Paul Leonard Senior Institute Research Scientist MD Anderson Cancer Center 1881 East Road Houston TX 77054 USA 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.

1 0

Rebuild in place - Phenix AutoBuild
by Emad Alharbi 15 Sep '20

15 Sep '20

Dear Phenix developers, I have a question about using 'Rebuild in place' feature in Phenix AutoBuild. Which is recommended when you build MR case, set this feature to false or use the default option? I mean by saying default option to let Phenix AutoBuild decide. Thank you! ------------------------------ Emad Alharbi Research Student Department of Computer Science University of York,UK.

2 1

Phenix and Coot v0.9
by Cygler, Miroslaw 15 Sep '20

15 Sep '20

Hi, I recently switched to Coot v0.9. When I start refinement now, the Coot starts and window opens but the model and density are not uploaded there and no phenix extensions show. I wonder is this is something that I can fix on my mac laptop or a bigger issue requiring work of phenix developers? Best, Mirek

2 2

Improving Ramachandran plot
by Reza Khayat 09 Sep '20

09 Sep '20

Hi, I'm trying to follow the protocol described in White et al., Structural principles of SNARE complex recognition by the AAA+ protein NSF e-life 2018 https://elifesciences.org/articles/38888 Here is the pertinent paragraph: "To improve the Ramachandran statistics and geometry of the models, a two-parameter grid search of real space refinements was performed in which 3-5 macrocycles of global minimization and local grid search were performed in the presence of secondary structure restraints. First, a grid refinement search was performed for both target functions with around 1000 refinements each. For the emsley target function, rama_weight and scale_allowed were varied from 0.01 to 300; for the oldfield target function, a grid of refinements was performed over plot_cutoff values from 0.01 to 1.0 and weight_scale values from 0.1 to 300. Results were judged empirically and based primarily on a balance between CCmask and a minimal fraction of residues flagged by the program CaBLAM (Richardson et al., 2018<https://elifesciences.org/articles/38888#bib37>) because focusing on the fraction of residues with favored CCmask and Ramachandran statistics alone often resulted in unrealistic models with serious problems (Figure 12<https://elifesciences.org/articles/38888#fig12>, Table 2<https://elifesciences.org/articles/38888#table2>)." There are no differences in the refined structures regardless of what parameters I change. Attached is the input file I use for phenix.real_space_refine (1.18.2?). Altering the oldfield weight_scale (0.1 to 300) and plot_cutoff (0.1 to 0.5) makes no difference. Any help is highly appreciated. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 4

project directories
by Arthur Glasfeld 09 Sep '20

09 Sep '20

I’ve changed computers recently and for administrative reasons had to change my userID. As a result, all of the directories containing my phenix projects have changed. Is there a simple way to update the directories associated each project? Thanks Arthur ***************** Arthur Glasfeld Reed College Portland, OR 97202

2 1

group on special position
by Arthur Glasfeld 04 Sep '20

04 Sep '20

I’ve run into a situation where I think I have a phosphate sitting on a 3-fold axis, where the P to O1 bond lies on the axis and the atoms O2, O3 and O4 are in symmetry-related positions. The data go to 1.6 Å, so it looks pretty convincing. I’m refining this in Phenix and have tried some tricks with occupancy - fixing the atoms at 0.33, but I get a lot of positive density in the Fo-Fc map and large B-factors. I’ve looked around but am not finding ideas on how to model this correctly in my structure file - the references I find are for monoatomic ions. Any advice would be welcome. Thanks, Arthur ***************** Arthur Glasfeld Reed College Portland, OR 97202 Office: (503)517-7679

3 6

General interest re research data
by John R Helliwell 01 Sep '20

01 Sep '20

Dear Colleagues, A couple of research data matters that I imagine will be of general interest I have placed at the IUCr CommDat Forum:- The Photon and Neutron EU Facilities Open Science Cloud announced their “doi per experiment” described in this 3 minutes youtube movie clip https://forums.iucr.org/viewtopic.php?f=39&t=431 Secondly, the Swiss Universities Bulletin have produced a special issue on Research Data Management, to which I have contributed an article on Open science and the reproducibility of the scientific record https://forums.iucr.org/viewtopic.php?f=39&t=432 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

1 0

Phenix User Workshop, 15th and 16th of September
by Paul Adams 31 Aug '20

31 Aug '20

Dear Colleagues, The Phenix developers will be holding an online Phenix User Workshop on the 15th and 16th of September at 8am-12pm PDT. These times will work best for researchers in North and South America, Europe and Africa. We plan to hold a future workshop at a time better suited to 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 crystallography and cryo-EM in Phenix, with the final emphasis based on the applicants’ research interests. To apply, send email to workshops(a)phenix-online.org with a short paragraph about your interests. 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. 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 250 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 ][ 1-510-486-5455 ] --

1 0

phenix.resolve_cryo_em
by Reza Khayat 25 Aug '20

25 Aug '20

?Hi, I'm running into a clipping issue with phenix.resolve_cryo_em. The program seems to be improving the map; however, portions of the map get clipped. Any suggestion would be appreciated. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

2 2

MicroED Imaging Center
by Johan Hattne 24 Aug '20

24 Aug '20

Dear Structural biology community; We are delighted to announce that the National Institutes of Health is helping us establish a Biotechnology Development Research Center focused on MicroED at UCLA School of Medicine, named MicroED Imaging Center (MEDIC). The main thrust of MEDIC is for method development and research focused on MicroED. As part of community engagement, the center will host the annual MicroED course as well as an annual MicroED Summit, both of which will be staged at the UCLA School of Medicine, and open to the community on a first come first serve basis until spaces are filled. Approximately 90% of available spots will be allocated to academic attendees and 10% to industry attendees. This will be a continuation of almost 10 years of tradition of providing workshops and training to the community. Also, there is some opportunity for the community to collect data on MEDIC microscopes. There is also limited availability for one-on-one user training at the center at UCLA for microscope set up and data collection. Users and trainees will be invited based on replies to a call for proposals, which will be advertised shortly. The proposals will be reviewed by an advisory committee. Because of the COVID19 pandemic and the limitations on travel and hosting imposed by UCLA we cannot begin these activities at this stage. On a related note, UCLA School of Medicine is also running a MicroED Imaging Core which is open as a pay per use service for academia and industry. This activity is independent of the Gonen Lab and from the NIH funded research program on MicroED. Details can be found online. Kind regards Tamir Gonen and Pawel Penczek

1 0

error while Auto sharpen
by sangeeta niranjan 19 Aug '20

19 Aug '20

Hello, I am trying to use Auto Sharpen feature of a CyoEM refined map into Phenix but the job is getting failed every time with the following error: Missing the model file: followed with model file name and location. Although it was working before but now it's showing the same error for all the auto sharpen runs including Models/PDBs. Thank you -- Sangeeta Niranjan Ph.D. Student, Lab of structural Biology Lab-6 NB National Centre for cell Science Ganeshkhind, Pune, India

2 1

moving folders
by Thomas, Leonard M. 18 Aug '20

18 Aug '20

Hello, I know this come up every so often by my google-fu is sorely lacking to find the answer. How does one move a project folder? I have a project and not thinking things through set it up in the wrong folder. I would like to move the whole thing to another folder maintaining the project structure. Thanks, 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

2 1

Phenix.Refine fix WXC has no effect
by White, Mark 17 Aug '20

17 Aug '20

Hello, I am refining a 3.5 Å structure using the latest stable version of Phenix.Refine. After switching to the latest version the Bond RMSDs exploded to ~ 0.035 Å, when using optimize wxc. Turning off Optimize and using the "Fix WXC" parameters in the GUI with increasingly smaller values had almost no effect on the final bond rmsds, which seems to explode from reasonable values in the "3_xyz" step of refinement. Am I missing something? Best regards, Mark Mark Andrew White, Ph.D. Associate Professor of Biochemistry & Molecular Biology, Manager, SCSB Macromolecular X-ray Laboratory UTMB, Galveston, TX http://xray.utmb.edu

4 4

Phenix.refine on coordinate-optimised structures
by Joey Farrell 08 Aug '20

08 Aug '20

Hello, I am trying to design a set of input parameters that I will be passing through the phenix.refine function. The structures that I am working with have already had their X,Y, and Z orthogonal Å coordinates optimised via separate protocol. I am looking for advice on which strategies and parameter values to use with phenix.refine to improve the crystallographic R-factors of such structures while preserving their earlier optimisation in real space. I have been having some success using “strategy = tls+individual_adp+occupancies” (where tls = “chain A”, tls = “chain B”, etc.) as well as adjusting the wxu_scale value until R-work and R-free are minimised. Are there other strategies or phenix.refine functionalities that may also prove helpful with this end in mind? I believe there may be ways to further improve R-work and R-free with this software that I am not yet aware of. Thank you for your help! Best, Joey

3 2

Phenix Real_Space_Refine and Torsion NCS restraints
by Mark A. White 04 Aug '20

04 Aug '20

Hello, Are there plans to include Torsion Angle NCS restraints in the Phenix.Real_Space_Refine module? At low resolution (~ 3-4Å) I would like to include NCS restraints, but my molecule is flexible and the strict NCS constraints used in the Real_Space_Refine module are not appropriate. I am currently using phenix-1.18.2-3874. Best regards, Mark

3 3

map to model - DNA model building
by Manoj saxena 04 Aug '20

04 Aug '20

Hello, I am trying to fit a cryo-EM map of a DNA protein complex (3.3 A) using the map to model in Phenix 1.18.2.3874, with a DNA sequence input in fasta format and the map as a .ccp4 file. However the output model fitted in the map I am getting is many fragmented PDB files and only one chain of DNA. What is the best way to get a higher fraction of the DNA model fitted into the map, can I switch off the segmentation of map and get both strands fitted into the map. Or the only option is to manually build? Thanks for your help Regards Manoj Saxena

2 2

Model moving out of map
by Shanti Pal Gangwar 04 Aug '20

04 Aug '20

Dear all, I am trying to refine a Cryo-EM map at a decent resolution. The model was fit into the map in chimera and refined against the same map in Real space refinement in Phenix but after the run, a significant part of the model moved out of the density. I would appreciate any suggestion/strategy to solve this issue. Thank you Shanti Pal

2 1

Postdoc position at UT Health Science Center, San Antonio, Texas
by Yogesh Gupta 03 Aug '20

03 Aug '20

The laboratory of Dr. Yogesh Gupta at University of Texas Health Science Center in San Antonio is seeking an enthusiastic Postdoctoral Fellow to study the structure and function of nucleoproteins in infectious diseases and cancer. We combine structural biology tools (X-ray, cryo-EM, NMR) with cell-based methods to address mechanistic questions and exploit this knowledge for drug development. Please visit below websites to learn about our research program – https://www.nature.com/articles/s41467-020-17496-8 *http://ccri.uthscsa.edu/YGupta.html <http://ccri.uthscsa.edu/YGupta.html>* Preference will be given to applicants with demonstrated experience in macromolecular crystallography. Candidates are expected to possess strong organizational, interpersonal skills, and ability to work as part of a team. An ideal candidate should hold (or soon expect to hold) a Ph.D. or equivalent degree in biochemistry/biophysics/structural biology and have no more than 2 years of postdoc experience. Salary is competitive. San Antonio offers affordable cost of living and there is no state income tax in Texas. If interested in applying, please send a short description of your research accomplishments, and CV with a list of 3 references to Dr. Yogesh Gupta (email: *guptay(a)uthscsa.edu <guptay(a)uthscsa.edu>*). The Greehey Children’s Cancer Research Institute is a unique specialized cancer research center focusing on basic and translational research in childhood cancer and occupies a state-of-the-art 100,000 sq. foot research facility on the university’s Greehey Academic and Research Campus. San Antonio is the nation’s seventh largest city and is located at the edge of the beautiful Texas Hill Country. San Antonio offers a rich, multi-cultural community, affordable cost of living, excellent weather and a thriving biomedical industry.* All Postdoctoral appointments are designated as security sensitive positions. The University of Texas Health Science Center at San Antonio is an Equal Opportunity/Affirmative Action Employer including protected veterans and persons with disabilities.* Thank you very much for your time. Yogesh -- Yogesh Gupta, PhD Assistant Professor of Biochemistry & Structural Biology PI, Greehey Children's Cancer Research Institute University of Texas Health Science Center 8403 Floyd Curl Drive, San Antonio, Texas, USA 78229 http://ccri.uthscsa.edu/YGupta.html

1 0

Fwd: Sanofi Postdoctoral Fellowship: Computational Scientist for Antibody Engineering (Greater Boston, MA)
by yanfeng zhou 01 Aug '20

01 Aug '20

If you have strong interest in one of the following areas, please continue to read and check the link for more details. 1. Developing new algorithms to revolutionize biologics discovery 2. Challenging yourself with large and unique datasets and converting your learnings to tools/products that can help patients 3. Engineering of antibody, nanobody, and other biotherapeutics modalities 4. Learning how scientists from various training backgrounds collaborate together to discover and deliver faster and better biologics treatments. The Protein Engineering group within Sanofi Large Molecule Research Department is seeking a highly talented Computational Scientist for a postdoctoral position. We use leading-edge structural biology and computational tools to support biologics project needs from Sanofi’s multi-targeting, multi-modality research pipeline. Our team has a great track record of patents and publications, including Science, Nature Cancer, and Nature Communications, in the area of biologics characterization, antibody engineering and multi-specific antibodies. This postdoc project will focus on developing a machine learning approach to predict epitope-paratope, given any antibody-antigen pair, by combining in-depth understanding of structure biology, antibody engineering, and large datasets both internally and externally. The successful candidate will be with Ph. D. degree in related area and has an advanced understanding and practical experience with developing and applying complex machine learning solutions for structural biology data. The successful candidate will gain deeper insight into drug development process and transform AI/ML algorithms into accelerating biologics discovery and development process. Application Link: https://sanofi.wd3.myworkdayjobs.com/en-US/StudentPrograms/job/Framingham-M… *About Sanofi:* Every day, Sanofi's 100,000 employees are committed to improve the lives of people around the world, with sustainable and responsible solutions and initiatives. Sanofi is recognized as one of the leading biopharmaceutical companies in the world and is pioneering innovation in biologics with the first approved nanobody drug, the first clinical stage tri-specific antibody, and a novel genetic codon expansion platform for new engineering capabilities. Details of the organization and the company’s mission and goals can be found on our website (http://www.sanofi.us/l/us/en/index.jsp). ------------------------------ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Yanfeng Zhou, Ph.D. Email: YanfengZhou.pku(a)gmail.com <yanfengzhou.pku(a)gmail.com>

1 1

postdoctoral position at the Institute for Protein Innovation in Boston, USA
by Christopher Bahl 29 Jul '20

29 Jul '20

The Bahl Lab <http://function-structure.org/> at the Institute for Protein Innovation (IPI) in Boston is recruiting Postdoctoral Fellows. We use protein design to accelerate drug discovery and to engineer new lead therapeutic molecules. In addition to traditional academic collaborations, we work closely with pharmaceutical and biotech companies, as well as venture capital firms. We are looking for translationally-minded scientists who want their work to have a direct impact on the world. We will provide training in computational protein design using Rosetta, including de novo protein design and the design of protein function and biophysical properties. Postdoctoral Fellows at IPI leverage our high-throughput automated laboratory infrastructure. We are especially excited to expand our work in the following research areas: - prediction and design of protein developability for therapeutic applications - engineering of de novo miniprotein/peptide lead therapeutics for oncology, infectious disease, hypertension and diabetes, etc. - antibody design, including de novo paratope design - enzyme design Strong candidates will have demonstrated expertise in one or more of the following: - protein biochemistry: protein production and biophysical characterization, enzymology - structural biology: cryo-EM, X-ray crystallography, NMR - immuno-oncology: cell culture models, fluorescence activated cell sorting - traditional protein engineering: directed evolution, library construction, yeast and/or phage display - computational biology: machine learning, data science, molecular dynamics and/or modeling If you are excited to join a team of protein designers working to tackle audacious projects aimed directly at improving human health, please send your CV to: chris.bahl(a)proteininnovation.org About IPI The Institute for Protein Innovation is a non-profit organization that is advancing protein science to accelerate research and improve human health. The Institute is located at Harvard Medical School. IPI uniquely combines the freedom of academic exploration with the high-throughput scaling of industry to take on transformative protein-based initiatives that no other laboratory or organization can or will pursue. IPI is deploying state-of-the-art technologies to build a repository of powerful protein tools and reagents and share them through licensing and collaboration. These will enable new biomedical and therapeutic discovery for researchers in academia and industry alike. This constellation of vanguard technology and expertise positions IPI to train the next generation of entrepreneurs and protein scientists to lead the discovery of new medicines. The IPI is an equal opportunity employer and prohibits discrimination based on ethnicity, religion, sexual orientation, gender identity/expression, national origin/ancestry, age, disability, socioeconomic status, marital or veteran status, etc. Candidates from underrepresented backgrounds are especially encouraged to apply. -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you.

1 0

Re: [phenixbb] Phaser-MR output after each component placement
by Randy Read 28 Jul '20

28 Jul '20

Hi Boaz, At the moment, that is indeed the only thing you can do with the partial solution information from the log file. In the CCP4 environment, you can cut and paste lines from the log file to make a .sol file, and use that to run something like a refinement job to produce a PDB and MTZ for a partial solution, but the Phenix environment uses Python pickle files to store the transformations, so that option doesn’t apply. (Unless you run Phaser from a script, in which case the Phenix and CCP4 versions work the same.) At one point, Phaser was writing out a PDB file for the top solution at every point in the process, but we felt that led to clutter and that it was confusing. There’s a major rewrite going on at the moment, and the new phasertng will primarily be run through the phaser.voyager pipeline. One of the design criteria here was to be able to examine branches that weren’t taken or intermediate points in the ongoing search, and to be able to work with them while the overall job is still running. So there will be a better option in the hopefully not too distant future! Best wishes, Randy ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > On 27 Jul 2020, at 23:02, Boaz Shaanan <bshaanan(a)bgu.ac.il> wrote: > > Hi, > The closest option that comes to mind to do what you're looking for is to take the Euler angles+translations for each of the monomers in the .sol file (or at the top of the final pdb file) and apply each of them to the initial model using any transformation program of your choice. > I am more familiar with running Phaser using the ccp4 gui but it shouldn't be very different under Phenix. > Phaser people may well suggest a more elegant option. > Stay safe, > Boaz > > Boaz Shaanan, Ph.D. > Department of Life Sciences > Ben Gurion University of the Negev > Beer Sheva > Israel > > On Jul 27, 2020 16:02, Johannes Cramer <johannes.cramer(a)gmail.com> wrote: > Dear phenix board, > > does anyone of you know if there is an option in phaser-MR to output a pdb after each placed component? > For example: I suspect there to be 5 molecules in the AU. I start a replacement with 5 molecules and phaser places 1 (I would like to inspect that), 2 (again, I would like to look at the e.g. top 10 results), 3 and so on... > Is that possible? I couldn't find the option in the gui or in the phenix documentation, but maybe in the CLI? > I know I can run one after the other, but that would potentially waste CPU time until I find time to inspect them. > > Cheers, > Johannes > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

2 1

Visiting Research Specialist Position at the University of Illinois to Study Ribosome Structure
by Yury Polikanov 28 Jul '20

28 Jul '20

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 *Visiting Research Specialist* 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's research can be obtained from the most recent publications ( https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/503…) or found on the laboratory 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:* - BS degree in chemistry, biochemistry, biophysics, or a related field; - MS degree or higher is preferred; - Minimum 3 years of laboratory research experience; - Strong background in biochemistry and molecular biology; - Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); - Experience in structural biology (cryo-EM or X-ray crystallography) is desired; - Experience in RNA biology is 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. For fullest consideration, please submit an application and cover letter describing your scientific interests and how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group at https://jobs.uic.edu/job-board/job-details?jobID=133847 by August 14, 2020. The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans, and individuals with disabilities are encouraged to apply. The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act.

1 0