- phenixbb - phenix-online.org

executing Phenix in a python script on a Windows OS
by Muriel Gelin 01 Mar '21

01 Mar '21

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.

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on rosetta installation for phenix use
by Smith Lee 28 Feb '21

28 Feb '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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Collection of articles from ISDSB2019 now published in IUCr Journals
by John R Helliwell 26 Feb '21

26 Feb '21

Dear Colleagues, A collection of articles from the International Symposium on Diffraction Structural Biology 2019 held in Osaka is now online in IUCr Journals at https://journals.iucr.org/special_issues/2021/ISDSB2019 Several of these articles are open access. Best wishes, Atsushi Nakagawa, John Helliwell and Yuriko Yamagata

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NCS/pseudo-symmetry
by Muhammad Bashir Khan 25 Feb '21

25 Feb '21

Dear All; *I collected data set which can be easily processed in a space grouop P21 (P1211)* *at approx 3.7A. I procedeed with MR using phaser in phenix which give a solution with two copies. * ** There were 8 solutions ** Pdb and/or Mtz files have been written with results for 1 of these solutions ** Solution #1 written to PDB file: Khan_phaser.1.pdb ** Solution #1 written to MTZ file: Khan_phaser.1.mtz Solution #1 annotation (history): SOLU SET RFZ=3.4 TFZ=4.2 PAK=0 LLG=15 TFZ==5.5 RFZ=2.8 TFZ=27.6 PAK=5 LLG=1173 TFZ==36.5 LLG=1210 TFZ==36.8 PAK=6 LLG=1210 TFZ==36.8 SOLU SPAC P 1 2 1 SOLU 6DIM ENSE ense_1 EULER 7.6 86.4 3.3 FRAC 0.20 0.00 0.18 BFAC -1.90 #TFZ==5.5 SOLU 6DIM ENSE ense_1 EULER 7.6 86.4 3.2 FRAC 0.05 0.00 0.51 BFAC 1.60 #TFZ==36.8 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0444 #RMSD 1.29 #VRMS 1.64 Solution #2 annotation (history): SOLU SET RFZ=3.0 TFZ=5.5 PAK=0 LLG=10 RFZ=2.7 TFZ=25.6 PAK=0 LLG=1165 TFZ==34.8 LLG=1198 TFZ==34.0 PAK=4 LLG=1198 TFZ==34.0 SOLU SPAC P 1 2 1 SOLU 6DIM ENSE ense_1 EULER 10.7 83.5 177.9 FRAC 0.24 -0.00 0.14 BFAC -3.15 SOLU 6DIM ENSE ense_1 EULER 169.3 96.4 357.9 FRAC 0.91 -0.00 0.52 BFAC 1.82 #TFZ==34.0 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0705 #RMSD 1.29 #VRMS 1.65 Solution #3 annotation (history): SOLU SET RFZ=3.4 TFZ=4.1 PAK=1 LLG=-1 RFZ=2.8 TFZ=34.6 PAK=1 LLG=1146 TFZ==39.7 LLG=1185 TFZ==39.2 PAK=3 LLG=1186 TFZ==39.2 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 8.2 86.4 2.0 FRAC 0.01 -0.00 0.01 BFAC -1.69 SOLU 6DIM ENSE ense_1 EULER 8.3 86.4 2.0 FRAC -0.14 -0.00 0.34 BFAC 1.72 #TFZ==39.2 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0406 #RMSD 1.29 #VRMS 1.64 Solution #4 annotation (history): SOLU SET RFZ=3.5 TFZ=5.0 PAK=6 LLG=13 RFZ=2.9 TFZ=30.5 PAK=6 LLG=1156 TFZ==34.4 LLG=1183 TFZ==33.6 PAK=7 LLG=1183 TFZ==33.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.5 82.0 2.7 FRAC -0.18 -0.00 0.47 BFAC -2.89 SOLU 6DIM ENSE ense_1 EULER 359.5 82.1 2.8 FRAC -0.02 -0.00 0.14 BFAC 2.57 #TFZ==33.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0529 #RMSD 1.29 #VRMS 1.64 Solution #5 annotation (history): SOLU SET RFZ=3.5 TFZ=5.0 PAK=6 LLG=13 RFZ=3.0 TFZ=29.0 PAK=6 LLG=1115 TFZ==34.1 LLG=1178 TFZ==33.6 PAK=7 LLG=1178 TFZ==33.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.9 80.8 0.7 FRAC -0.18 -0.00 0.47 BFAC -1.57 SOLU 6DIM ENSE ense_1 EULER 180.1 99.2 180.7 FRAC 0.34 0.50 0.20 BFAC 2.47 #TFZ==33.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0405 #RMSD 1.29 #VRMS 1.64 Solution #6 annotation (history): SOLU SET RFZ=3.5 TFZ=4.6 PAK=1 LLG=-0 RFZ=2.8 TFZ=36.2 PAK=1 LLG=1136 TFZ==35.0 LLG=1169 TFZ==34.6 PAK=1 LLG=1169 TFZ==34.6 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.2 83.0 1.5 FRAC 0.06 0.01 0.03 BFAC -2.58 SOLU 6DIM ENSE ense_1 EULER 359.2 82.9 1.4 FRAC -0.09 0.01 0.36 BFAC 2.08 #TFZ==34.6 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0869 #RMSD 1.29 #VRMS 1.66 Solution #7 annotation (history): SOLU SET RFZ=3.5 TFZ=4.6 PAK=1 LLG=-0 RFZ=2.8 TFZ=35.3 PAK=1 LLG=1122 TFZ==35.4 LLG=1149 TFZ==34.5 PAK=1 LLG=1148 TFZ==34.5 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 359.2 82.5 2.4 FRAC 0.06 0.01 0.03 BFAC -1.93 SOLU 6DIM ENSE ense_1 EULER 180.8 97.5 182.4 FRAC 0.78 -0.49 0.31 BFAC 2.44 #TFZ==34.5 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0809 #RMSD 1.29 #VRMS 1.65 Solution #8 annotation (history): SOLU SET RFZ=3.4 TFZ=4.1 PAK=1 LLG=-1 RFZ=2.8 TFZ=33.9 PAK=1 LLG=1083 TFZ==38.5 LLG=1146 TFZ==38.5 PAK=4 LLG=1146 TFZ==38.5 SOLU SPAC P 1 21 1 SOLU 6DIM ENSE ense_1 EULER 8.1 86.1 2.6 FRAC 0.01 -0.00 0.00 BFAC -1.77 SOLU 6DIM ENSE ense_1 EULER 8.1 86.2 2.6 FRAC 0.17 -0.00 -0.33 BFAC 1.66 #TFZ==38.5 SOLU ENSEMBLE ense_1 VRMS DELTA +1.0762 #RMSD 1.29 #VRMS 1.65 CPU Time: 0 days 6 hrs 35 mins 53.63 secs ( 23753.63 secs) Finished: Tue Feb 16 23:27:36 2021 *Got the following warnings:* WARNINGS -------- ------------------------------------------------------------------------------------------ Warning: Intensity moments suggest possibility of twinning. Tests based on possible twin laws will be more definitive. ------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------ Warning: The composition you have entered gives a solvent content of 87%, which is extremely unlikely. You should increase the composition. After running xtraige for the .mtz, I get this warning about NCS Frac. coord. : 0.157 -0.000 -0.333 Distance to origin : 119.294 Height relative to origin : 33.056 % p_value(height) : 8.504e-04. Translational pseudo-symmetry is very likely present in these data. Be aware that this will change the intensity statistics and may impact subsequent analyses, and in practice may lead to higher R-factors in refinement. Upon an attempt at initial refinement with different stratageis, the R-fators are stuck at Start R-work = 0.5066, R-free = 0.5233 Final R-work = 0.4831, R-free = 0.4965 The question is that there is something that is not being recognized for example merohedral twinning or that the NCS/pseudosymmetry is not being addressed correctly. Any suggestions would be highly appreciated. Regards; 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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Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)
by Bjørn Panyella Pedersen 25 Feb '21

25 Feb '21

Dear colleagues, We have an open postdoc position. 3 days left before deadline. Come joint us. Great working environment, World-class science. Good work/life balance. /Bjørn ----------------------------------- Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. online posting: https://tinyurl.com/MBGpostdoc We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021.

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EMBO workshop on Molecular Neurobiology
by Janssen, B.J.C. (Bert) 24 Feb '21

24 Feb '21

Dear all, a gentle reminder of the upcomingEMBO workshop on "Molecular Neurobiology", a virtual meeting taking place on 21-25 May 2021. The deadline for registration, 28 February, is approaching fast. Only four days left. The virtual meeting brings together world leading scientists, group leaders and young researchers with a keen interest in the latest science occurring at the interfaces of structural biology, biophysics, molecular & cellular imaging and neuroscience. Given its cross-disciplinary nature, the meeting presents a broad overview of molecular neurobiology, ample opportunities for discussions and a sneak peek into the latest developments. See http://meetings.embo.org/event/20-molneuro for more information and application guidelines. Best wishes, Bert Bert Janssen Bijvoet Center for biomolecular research Utrecht University Padualaan 8, 3584 CH, Utrecht

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reminder - postdoc position at Astex
by Gabor Bunkoczi 23 Feb '21

23 Feb '21

Dear All, Just a quick reminder that Astex has an opening for a skilled post-doctoral researcher with an interest in software development. The aim of the project is to develop new methods for automated ligand fitting guided by experimental electron density/electrostatic potential maps, and will focus on locating, sharpening and classifying unmodelled regions of density, determining the identity of the binder using density shape and other physical properties derived from the surroundings, and subsequently fitting the molecule taking potential interactions with the environment into account. For more information about the position, please see the full advert: https://astx.com/wp-content/uploads/2021/01/SI-Post-Doc-2019-Mol-Sci-new-ad… Interested candidates should liaise with the HR department. For informal enquiries, please feel free to contact me directly. Best wishes, Gabor Bunkoczi Astex Therapeutics Ltd 436 Cambridge Science Park Cambridge CB4 0QA, UK This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.

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Virtual Annual CCP4/APS Crystallographic School (2021) in the US
by Xu, Qingping 22 Feb '21

22 Feb '21

Dear Colleagues, We are pleased to announce the virtual annual CCP4/APS crystallographic school "From data collection to structure refinement and beyond" will be held on June 14-25, 2021 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2021/index.php. Dates: June 14 through 25, 2021 (with a weekend break on June 19 and 20th) Location: Virtual/Remote The school comprises two parts: remote data collection workshop and virtual crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA at APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections - lectures, tutorials, and hands-on (interactive troubleshooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 1st, 2021. To apply, visit https://www.ccp4.ac.uk/schools/APS-2021/application.php. Fees: There is no fee for attending the virtual school for the chosen applicants. We hope to see you at the school. Charles, Garib and Qingping

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Re: [phenixbb] Autosol help: FOM is great but map is trash
by Kay Diederichs 19 Feb '21

19 Feb '21

Hi Alex, I'm not a Phenix developer, but I have seen many cases like this, where reflections can be indexed with different cells, and one unit cell axis differs by a factor of 2. This just means that every second reflection (namely the odd one) along the reciprocal space direction corresponding to that axis is weak. It is not a priori clear which of the two choices is the best for structure solution and refinement. This depends on whether the weak reflections actually carry structural information (e.g. about tNCS with a translation close to 0.5), or whether they are a result of a crystal defect. It may sometimes happen that the crystal form is not suitable at all, since both choices don't refine well! Concerning P212121, P21212, P2122, etc: these are all primitive orthorhombic, and data processing alone cannot tell you which one is correct - they give identical data processing statistics. Typically, absent reflections along h00 0k0 00l should tell about screw axes, but in case of tNCS and two different cell choices the correct choice may not be obvious. Molecular replacement and subsequent refinement of all possibilities should help. Furthermore, contrary to what you write, it _is_ possible for all the orthorhombic space groups to account for reflections in both cell choices, so don't jump to conclusions too early. Just explicitly specify the (big or small) cell parameters in the data processing program of your choice! It may also help to try a different data processing package. Hope this helps, Kay Am 19.02.2021 um 04:28 schrieb phenixbb-request(a)phenix-online.org: > Message: 4 > Date: Thu, 18 Feb 2021 18:15:15 -0500 > From: Alex Johnson<algejohnson(a)gmail.com> > To:[email protected] > Subject: [phenixbb] Autosol help: FOM is great but map is trash > Message-ID:<6BE0A20E-F46B-482A-A675-22B685A2AFBE(a)gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Phenix team, > > I am attempting to phase a protein structure from SeMet-labeled crystals and have encountered some issues in using Autosol that appear unusual, as they have not been encountered by any members of my group. The short summary is that while I achieved great statistics from beam line collection and Autosol produces solutions with FOM (>0.4) from multiple crystals processed to ~2.4-3.0 A, the output maps are of poor quality and Autobuild can never build with Rfree <0.5. There is only one methionine for the ~30 kDa protein, but the crystals appear to have good anomalous signal with anomalous multiplicity >15 overall and delanon in the inner shell >0.5. There appears to be translational NCS and the dataset can be processed with good statistics in several space groups (P212121, P21212, P2122, etc) but this doesn?t solve the phase problem. The axis drops by half in processing in the P212121 versus P21212 space groups: from one crystal they are 48.37 101.56 110.39 90 90 90 (in P212121) and 101 > .62 48.35 55.19 90 90 90 (in P21212). > > If anyone in the community has encountered similar problems please let me know! I am all ears to any possible solutions and am also installing additional methionine for labeling but unsure whether this will overcome the other issues. > > Thanks, > > Alex Johnson > Postdoc, Kranzusch lab, Dana-Farber Cancer Institute > algejohnson(a)gmail.com <mailto:[email protected]> > > > > > >

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Scientist Antibody Production at the Institute for Protein Innovation in Boston, USA
by Christopher Bahl 19 Feb '21

19 Feb '21

Scientist Antibody Production Reports to the Head of Biological Discovery, Dr. Rob Meijers The Institute for Protein Innovation (IPI) is a nonprofit research organization advancing protein science to accelerate research and improve human health. Located on the Harvard Medical School campus in the Boston Longwood Medical Area, IPI is pioneering a new way of doing science that uniquely combines the freedom of academia with the high-throughput scaling of industry to take on transformative projects. IPI has built a robust platform and a repository of synthetic antibodies and other protein tools to share with the biomedical community through licensing and collaboration. The Institute’s deep protein expertise, collaborative spirit and fit-for-purpose antibodies are powering new biomedical and therapeutic discoveries for academic and industrial researchers worldwide. Job Overview IPI’s flagship project, the “Antibody Initiative,” aims to create well-characterized, synthetic antibodies against human cell surface receptors and their ligands, particularly those that are traditionally difficult to target. These antibodies may have high therapeutic and diagnostic potential but will also serve to enable basic biological discovery. The Scientist, Antibody Production will play an essential role in the high-throughput production, characterization and formulation of synthetic antibodies for this Initiative and other key IPI projects. Specifically, the successful candidate will join the Protein Group, a dynamic team generating high-quality antibodies and developing new technologies for conjugation. Having completed a doctorate in protein chemistry, the successful candidate will bring to the job experience in mammalian expression, purification and reagent-grade preparation of glycoproteins. The candidate will be adept in quality control and process management and reliably provide detailed documentation on experiments completed. The Scientist will work in close collaboration with the other Antibody Initiative team members and enjoy the opportunity to contribute to a wide array of novel biological discovery projects. As this position is highly collaborative, strong communication skills are needed. The Scientist will engage with outside collaborators, translate their biological questions into novel protein reagents and share these reagents with the larger research community through abstracts, presentations and publications. Responsibilities and Duties -Express, purify, and characterize glycoproteins from mammalian cells -Leverage robotics and automation to increase the quality and throughput of antibody production at IPI -Formulate and package antibodies for use by collaborators and customers -Supervise research associates and coordinate with other scientists to ensure efficient, high-quality antibody production -Actively lead the experimental design and data production for collaborations and scientific publications -Participate in meetings and conferences to engage and recruit outside research groups to participate in the Antibody Initiative Qualifications -PhD degree in mammalian protein expression, protein biochemistry, or structural biology -Well acquainted with best practices in cell culture and reagent production -Ability to work in a fast-paced, intellectually challenging environment -Enthusiastic team member with a strong commitment to mission and a desire to conduct impactful science -Good organizational and documentation skills -The ideal candidate will have recently completed a PhD and have a desire to explore a more entrepreneurial position IPI is an independent 501(3)(c) nonprofit research organization and an equal opportunity employer. The Institute celebrates diversity and is committed to creating an inclusive environment for all employees. If interested, please email your resume to . -- 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.

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