- phenixbb - phenix-online.org

Phenix version 1.17 released
by Paul Adams 04 Nov '19

04 Nov '19

The Phenix developers are pleased to announce that version 1.17 of Phenix is now available (build 1.17.1-3660). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that there is a new publication that describes recent Phenix developments for structure determination with X-rays, neutrons and electrons: https://doi.org/10.1107/S2059798319011471 Highlights for the 1.17 version of Phenix: 1.17.1 Changes - Fix bug on Windows where xtriage results would fail to display - Other bug fixes 1.17 Changes - Improved handling of SHELX data in phenix.reflection_file_converter - eLBOW can output files for Amber and supports the Orca QM package - dials.image_viewer is used for viewing diffraction images - Updated map smoothing - Fix inconsistency in clashscore values in phenix.validation_cryoem when hydrogens are in the model For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (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: Nikki Humphreys [ nhumphreys(a)lbl.gov ][ 1-510-486-4610 ] --

1 0

Postdoc position available in LBNL
by Peter Zwart 31 Oct '19

31 Oct '19

Dear All, We have a postdoc position available at LBNL to work on the development of computational approaches for twinned crystallographic data. This is an exciting opportunity to address a relatively common phenomenon in crystallographic data analysis for which there are currently limited twinning-aware approaches. The aim is to develop tools that impact substructure solution, molecular replacement, density modification and structure refinement. Click the link below for more info or contact me directly. https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480 Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

1 0

Understanding Biology through Structure 16-20 March 2020
by Tom Terwilliger 30 Oct '19

30 Oct '19

Hi Colleagues, particularly students and postdocs, I would like to encourage you to sign up for "Understanding Biology through Structure 2020" (https://cvent.me/4kq9P, March 16-20, 2020 in Santa Fe,NM). Student and postdoc fellowships covering registration and hotel are available (awarded competitively after registration on a rolling basis). The conference is a forum where students and postdocs can meet established researchers and discuss the latest methods and results. For a one-line review and info on the last one see https://bit.ly/2Gfkm4t and https://bit.ly/2Gg39rm. Confirmed speakers are Ilme Schlichting, Yvonne Jones, Hao Wu, Peijun Zhang, Christopher Russo, Claudio Ciferri, David Stuart, Blake Wiedenheft, Ci Ji Lim, Robert Stroud, Wayne Hendrickson, Bonnie Murphy, Anne Houdusse-Juille, Sonja Lonrenz, Chris Hill, Chun-wa Chung, Jian Payandeh, Amit Sharma, Marissa Matsumoto, Suzanne Scarlata, Osamu Nureki, Natalia Jura, Erica Ollmann Saphire, Eva Nogales, Andrej Sali, Anke Bill, Joanna Sulkowska, David Eisenberg, Marie Pancera, Karla Satchell, Jacques Philippe Colletier, Tom Terwilliger, Christopher Neale, and Tom Blundell. All the talks will be followed by 10-15 minutes of discussion with participation by students and postdocs especially encouraged. After the main conference there will be an optional Phenix workshop with lectures and hands-on sessions on using Phenix for crystallography and cryo-EM. Registration is first-come first served, with a limit of 120. All the best, Tom T -- 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

1 0

GUI reorders file data type in EM validation task
by Ashley Pike 30 Oct '19

30 Oct '19

Hi, I am having problems convincing the GUI which EM map is which for halfmap validation. Version is 1.17-3644 Here is input: [cid:[email protected]] and what is written to Summary tab: [cid:[email protected]] Any tricks to getting this to work? Editing the .eff file written by the gui is an option but running phenix.validation_cryoem on the command line doesn't seem to produce much viewable output. Cheers, Ashley -- Dr. Ashley Pike Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford Phone: +44 (0)1865 617576 | FAX: +44 (0)1865 617575 | ashley.pike(a)sgc.ox.ac.uk<mailto:[email protected]> | www.thesgc.org<http://www.thesgc.org/> Address: Structural Genomics Consortium, Old Road Campus Research Building, Headington, Oxford OX3 7DQ, UK

2 2

Potential Berkeley Server Outage (October 25)
by Billy Poon 29 Oct '19

29 Oct '19

Hi everyone, As a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will probably be shut down today and will return next week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- 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 2

Berkeley Server Outage (Starting October 26th)
by Paul Adams 25 Oct '19

25 Oct '19

Dear Colleagues, yet again, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down this weekend and will return later the following week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) 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: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

1 0

real space refine and nonbonded_weight
by Cheung, Alan 25 Oct '19

25 Oct '19

Dear Developers A structure we refined back in 2017, using phenix.real_space_refine on a cryoEM map @ 3.7A (version 1.11.1–2575) produces a clashscore of ~8 but the exact same refinement run with the latest phenix (version 1.17.1) generates a clashscore of ~22. Our refinements with the latest version on other EM structures tend to generate pretty high clashscores too. I think i've tracked this down to the nonbonded_weight parameter, which defaults to 1000 in the older version, and to 100 in the latest version. At which version did the default change, and is there a reason for it? I couldn't find it in the changelog. Alan

2 1

rosetta.run_tests crash
by wtempel 25 Oct '19

25 Oct '19

Hi, has anyone tried the combination of phenix-1.17 and rosetta-2019.40? Crashes in my hands, crash log attached. I may have modified the phenix installation by phenix.python -m pip install readline, in case it matters. Any suggestions appreciated. Many thanks in advance. Wolfram Tempel

2 1

Yeast microtubule model
by Sebastiano Pasqualato 24 Oct '19

24 Oct '19

Dear all, I’m addressing to people working in the microtubule field. Has someone created, or knows where I could find, a pdb file of the yeast microtubule, or a portion of it? I’m interested in studying the contacts between subunits within the lattice. I know one could generate that using yeast tubulin dimers, but I don’t know exactly how. If someone has already done that and is willing to share it, that would be extremely helpful. Thanks a lot in advance, ciao, S PS: sorry for the cross posting to members of both bulletin boards. -- Sebastiano Pasqualato, PhD Biochemistry and Structural Biology Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

1 0

Phenix-RSR model fit issue in CS-Map
by pramod kumar 23 Oct '19

23 Oct '19

Dear Experts, I have a map generated through cryosparc (ab initio-reconstr and homo-refine at 3.7A* FSC and sharpened in Scipion and separately in EMAN2). I have build the initial pdb through BALBES which has perfect validation parameters and nice fitting in the map (with the mtz output) but the co-ordinates are shifted from the true origin of CS-map. I used phenix-RSR to fit and refine, but validation results remained too far to accept the model as good solution and also a small region entered in wrong nearyby densities. So far following independent and downstream approaches I have taken:- In phenix; dock in map, map to model, rigid body refine followed by real space refine (with both .map and converted .mtz), using only chain A-map boxing and model generation through NCS. I have tried chimera fit for entire assembly and also only one chain in boxed map and full map but still the validation remained far from acceptable values and a small region in wrong neighboring density. Please help. -- Best regards, Promod

2 2

errors in rosetta.refine
by Bram mylemans 18 Oct '19

18 Oct '19

dear I am trying to run rosetta.refine but get an error. I am using the latest version of phenix (1.17-3644) and I have tried to versions of rosetta (3.10 release date 2 Oct 2018 and 3.11 release date 26 Sept 2019) If I run rosetta.run_tests with rosetta 3.10 I get the following error message: DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) If I run with rosetta 3.11 I get a different error message: DEBUG dumping error message ERROR: Rosetta exited with status 127 stderr output: /opt/rosetta_3.11_phenix/main/source/bin/rosetta_scripts.python.linuxgccrelease: error while loading shared libraries: libcifparse.so: cannot open shared object file: No such file or directory Are these version of rosetta and phenix compatible?

1 0

Small Molecule Discovery RFP - Deadline is October 28th
by Nick DeHaan 17 Oct '19

17 Oct '19

Hi PhenixBB, I thought this group might be interested in an academic research support program that helps identify new active compounds based on protein structure. The award provides investigators, postdocs, or grad students with approximately 72 small molecules predicted by machine learning to bind to their protein of interest. A few awards also provide in-kind support (with a value of up to $20k) for the assay work. Applications take ~30 minutes to complete, and >300 awards will be given out this cycle. Proposals are due by October 28th. You can find out more here: Website: www.atomwise.com/aims <http://bit.ly/31rz1B4> Infographic: http://www.atomwise.com/wp-content/uploads/2019/10/AIMS-Infographic-Stats_F… <http://bit.ly/31jRa3O> Flyer: http://www.atomwise.com/wp-content/uploads/2019/10/Atomwise-AIMS-Awards-Fly… <http://bit.ly/31nkVAI> Please feel free to reach out to me with any questions! Best regards, Nick Nick DeHaan, MsE *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

1 0

Job opening: Scientist-I (Structural Biology) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 17 Oct '19

17 Oct '19

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology. The candidate will join the structural biology group within the NCI RAS Initiative program and work on the 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 Leidos Biomedical Research, Inc. *Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701 *USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

1 0

high B Factor after real space refinement against a cryoEM map
by Keda Zhou 17 Oct '19

17 Oct '19

Dear all, I am trying to do the real space refinement for my model against a 5.0 angstrom cryoEM map. All parameters look pretty good except the B factor. The mean of the B factor is close to 400. I am just wondering whether the low resolution makes the B factor this high. Does anyone have any idea or suggestion on the high B factor during real space refinement? Is it possible to reduce it? What is the actual meaning of this B factor? Thanks in advance. cody

2 1

Two tenure-track faculty openings at Univ. of Missouri Biochemistry
by Tanner, John J. 14 Oct '19

14 Oct '19

Dear Colleagues, My department has two tenure-track faculty openings. Review of applications will begin on November 15, 2019. Click the link below for more information. https://biochem.missouri.edu/open-positions/ 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]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

1 0

file location changed
by Cygler, Miroslaw 14 Oct '19

14 Oct '19

Hi, In order to allow synchronization of files on my mac with the cloud server I had to move all files used by Phenix to a new directory, including the main Phenix folder. How do I change the paths to these files in phenix so that they are accessible to the software? Phenix would not start without the main Phenix folder returned back to the old location. How do I rectify this as well? Thanks for your help, Mirek

2 1

advert for PostDoc position @Singapore
by SR Bharath 14 Oct '19

14 Oct '19

Dear Colleagues, We are seeking an enthusiastic and self-motivated postdoctoral research fellow to study proteins involved in maintaining genome stability and the Hippo signaling pathway. We take a combinatorial approach of molecular biology, biochemical and biophysical methods, and structural biology (macromolecular crystallography and electron cryomicroscopy). Significant aspects of our projects have translational potential. The candidate is expected to be involved in the development of small molecules/peptides for cancer therapeutics. Singapore is an excellent environment to do research with many research groups close by in Biopolis [https://www.a-star.edu.sg/imcb]. A*STAR offers highly competitive salaries with benefits including housing allowance and 1-3 months performance bonus. Requirements: · PhD in biochemistry, biophysics, molecular & cell biology or in medicinal chemistry · Practical experiences in structural biology (Electron Cryomicroscopy and/or X-ray crystallography) or in medicinal chemistry · Good publication record · Competent in scientific writing Interested applicants should send a CV and three confidential letters of reference to: Prof. Haiwei Song (Email: *haiwei(a)imcb.a-star.edu.sg <https://webmail2.imcb.a-star.edu.sg/owa/redir.aspx?C=EzRllkOmnk2jjotDLR8t5a…>*), Institute of Molecular and Cell Biology, A*STAR, Singapore. Cheers, Bharath

1 0

Masked FSC estimation failure
by ze li 12 Oct '19

12 Oct '19

Hello: I have three cryo-ET full maps, not in halves, to estimate their resolutions. I intended to estimate the resolution of the maps with the high-resolution models in the PDB databank. Is it the best to get a map to model FSC estimation at 0.5 cut-off? I calculated three maps with cryo-EM module in Phenix, but only one gives the masked and unmasked curves, the other two only have the unmasked results.I tried many times but failed to figure out the questions of these two maps. What is the possible reason for them? Or Is there any other ways to get the unmasked and masked FSC? Thank you for your help. Sincerely, Ze

1 0

Berkeley Server Outage (Starting October evening 8th)
by Paul Adams 12 Oct '19

12 Oct '19

Dear Colleagues, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this week meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down today and will return later in the week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) 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: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

2 1

University of Maryland/Open-Rank Tenure-Line Faculty Position
by Hasan, Syed Saif 09 Oct '19

09 Oct '19

Dear Colleagues, The Institute for Bioscience & Biotechnology Research (IBBR) and the University of Maryland, College Park Department of Chemistry & Biochemistry invite applications for an open-rank, tenure-line faculty position in structural biology, with an emphasis in the area of biomolecular cryo-electron microscopy, starting August 2020. A detailed ad is attached to this email. Applications, consisting of a cover letter, curriculum vitae, statement of research plans, statement of educational interests, and three references, must be submitted electronically at: https://ejobs.umd.edu/postings/74094 Review of applications will begin November 15, 2019. We will continue to accept applications until the position is filled. Direct inquiries and/or nominations to the chair of the search committee, at: cryoemsearch(a)ibbr.umd.edu Saif S. Saif Hasan, PhD https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ https://www.ibbr.umd.edu/profiles/s-saif-hasan

1 0

positional restraints in real_space_refine?
by Daniel Larsson 08 Oct '19

08 Oct '19

Hi all, I'm working on a cryo-EM reconstruction where I have some flexible low-resolution elements (RNA double helices). They have different orientations relative to my reference model, but I would like to model them in the approximately correct position. I've tried real_space_refine with morphing and simulated annealing, but neither accomplish what I want. Now I'm thinking of cutting out these helices and manually position them approximately where I want them. But I fear that this will case headache at the "joint". Is it possible to use the manual positions as a reference for positional restraints, but use the original model as the reference for the torsion angles. Is this possible with real_space_refine? Or is there a better way of refining this structure? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 5

Phenix 1.17-3644 installation problems
by Hernando J Sosa 08 Oct '19

08 Oct '19

Dear Phenix developers, Trying to install Phenix in a Linux computer (OpenSuse Leap 15.1)I got the error messages listed below. Any help to fix this problem(s) would be appreciated. Thks. H. Precompiling .py files... Generating SOLVE/RESOLVE license file... Rebuilding HTML documentation... Error rebuilding documentation! Creating rotamer/Ramachandran database files... Traceback (most recent call last): File "./bin/install.py", line 244, in <module> installer(sys.argv[1:]).install() File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 201, in install self.install_finalize() File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 542, in install_finalize self.product_specific_finalize_install(log) File "./bin/install.py", line 130, in product_specific_finalize_install call([os.path.join(self.build_dir, 'bin', 'mmtbx.rebuild_rotarama_cache')], log=log) File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/hsxx/Programs/Phenix/phenix-1.17-3644/build/bin/mmtbx.rebuild_rotarama_cache' failed with exit code -4

2 1

reference torsion restraints for nucleic acids in real_space_refine
by Daniel Larsson 07 Oct '19

07 Oct '19

Hi all, In phenix.real_space_refine, I'm using a reference model for torsion restraints for a RNA/protein complex. I noticed in the log file under the section "Adding Reference Model Restraints (torsion)" that only the amino acid residues and some modified nucleotides are listed in the "Reference Model Matching Summary" but not the standard nucleotides. Does this mean that they are not restrained? I checked the _initial.geo file and there are no torsion restraints for the standard nucleotides in the "Reference torsion angle restraints" section. Are they not supported by default? My workflow was this: run ready_set on the initial model and then supply real_space_refine with a reference model and the ready_set cif file with the ligands. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

2 1

Base-pair restraints and high resolution cryoEM maps
by Stephen Cusack 07 Oct '19

07 Oct '19

Dear All, (1) Is it possible to add RNA base-pair restraints into Phenix Real-space-refinement of a lowish resolution cryoEM structure? If so how? (2) We are also lucky enough to have some impressively high resolution cryoEM maps (2.4 A average) which show among other things hundreds of water molecules. I was wondering whether Phenix Real-space-refinement was really adapted to high resolution, e.g. it uses grouped B-factor refinement and has no water handling options (putting them in manually is a pain and you always miss some). How have other people dealt with these issues ? thanks for any help Stephen Cusack -- ********************************************************************** Dr. Stephen Cusack, FRS Head of EMBL Grenoble Group leader in the structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr, stephen.cusack(a)embl.org Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

2 1

PhD and postdoc position - Structural Biology Methods development at Wuerzburg University
by Andrea Thorn 07 Oct '19

07 Oct '19

Dear colleagues, for two projects in structural biology methods development, we are looking for a PHD CANDIDATE (m/f/d) and a POSTDOCTORAL RESEARCHER (m/f/d) The Thorn Laboratory the Rudolf Virchow Center at the University of Wuerzburg develops new methods for macromolecular X-ray crystallography and Cryo-EM. In these exciting projects you will improve how well we understand, measure and model macromolecular crystal structures using practical experiments and big data analyses. We are looking for candidates with skills in data analysis and programming. Any previous experiences in crystallography, molecular biology, machine learning, image or statistical analysis are also a bonus. You should be a good communicator. For the PhD project, we offer a 36-month full- or part-time position, embedded in the Würzburg Graduate School for Life Sciences (GSLS); for the postdoctoral position, we offer a 30-month full- or part-time position with a competitive salary as well as career and family support. Women are particularly encouraged to apply. For more details, see: https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_PhD_Tho… https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_Postdoc… If you have any questions, please email me: andrea.thorn(a)uni-wuerzburg.de. Best wishes, Andrea Thorn. _____ Dr. Andrea Thorn group leader Rudolf Virchow Center for Experimental Biomedicine University of Wuerzburg Josef-Schneider-Str. 2 97080 Wuerzburg Germany andrea.thorn(a)uni-wuerzburg.de https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/tho…

1 0