- phenixbb - phenix-online.org

(no subject)
by Fulvio Saccoccia 27 May '14

27 May '14

Dear phenix users and developers, in the past I usually used the fix_rotamers=true options to fix some residue issues. Now, this option is lacking (I currently use the dev-1702 version of phenix) but I was wondering if some other option does replace it. In addition, I would like to know better how real_space_refinement works; is there any tutorial or presentation about it? Thanks in advance -- Fulvio Saccoccia, PhD Dept. of Biochemical Sciences Sapienza University of Rome 00185, Rome (Italy) Phone: +39 06 4991 0556 https://www.researchgate.net/profile/Fulvio_Saccoccia/?ev=hdr_xprf

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Workshop announcement @ Inst Pasteur Montevideo - Uruguay : Modern Approaches in Drug Discovery for Neglected Infectious Diseases
by Alejandro Buschiazzo 23 May '14

23 May '14

Dear Colleagues: We are pleased to announce the Workshop: "Modern Approaches in Drug Discovery for Neglected Infectious Diseases" at the Institut Pasteur de Montevideo (Uruguay). *Dates:* November 3rd - 8th, 2014 *Venue**: *Institut Pasteur de Montevideo (Montevideo, Uruguay) *Invited speakers:* Wim Hol (University of Washington, Seattle, USA), Paul Michels (University of Edinburgh, Edinburgh, UK), Celerino Abad-Zapatero (University of Illinois at Chicago, Chicago, USA), Hugo Cerecetto (UdelaR), Marcelo Comini (IP Montevideo), Sergio Pantano (IP Montevideo), Alejandro Buschiazzo (IP Montevideo)* * *Aim:* The general aim of this International Workshop is to train students in state-of-the-art approaches for drug discovery and rational design, with special emphasis on target-based methods. The course will provide with a multidisciplinary view, with invited professors covering a diverse set of subjects : protein crystallography, in silico methods for molecular simulations, medicinal chemistry and biology of neglected infectious diseases.** For details of the activity please see the preliminary program. <http://www.pasteur.edu.uy/images/program_v.5-5-14.2.pdf> The course will be in English. This activity is supported by the /Center for Structural Biology of the MERCOSUR /(CeBEM <http://www.cebem.org.ar/>), jointly with the /United Nations University Biotechnology Programme for Latin America and the Caribbean/ (UNU - BIOLAC <http://unu.edu/about/unu-system/biolac>). * **Applicants:* Graduate students and young research scientists are encouraged to apply. 24 students will be selected among the applications. The Course will provide financial support for the students, covering registration fees, and for the case of those coming from abroad, all local expenses (lodging, per diem and local transportation). /* The application deadline is September 8th, 2014. The results will be announced by September 30th.*/ The application form, activity program, contact information and other details can be found at the web site of the course <http://www.pasteur.edu.uy/index.php/en/teaching/courses/54-ensenanza/cursos…> Please address further inquiries toSBDD_course(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Three positions open at the MAX IV Laboratory
by Marjolein Thunnissen 22 May '14

22 May '14

The MAX IV facility, the largest and most ambitious Swedish investment in research infrastructure, will be the brightest source of x-rays worldwide and will replace the existing laboratory, which today consists of the storage rings MAX I, II and III. The new MAX IV facility will become operational in June 2016. To extend the suite of already funded beamlines, MAX IV Laboratory is planning the next set of beam lines. Therefore The MAX IV laboratory in Lund has opened two positions within the life-science division. We are looking for two beamline scientists, one for the biomedical imaging beamline MEDMAX and one for the microfocus beamline MicroMAX. For both these positions the scientist will be overseeing the development, construction and commissioning of the MedMAX, respectively MicroMAX beamline from its conceptual stage to full operation. Both beam lines are planned to be cutting edge beam lines, fully exploiting the excellent properties of the MAX IV 3GeV storage ring. In addition we are also looking for a software engineer to be engaged in the design of the MX software infrastructure at the beamline for protein crystallography which is under construction, BioMAX. More information on these positions can be found at https://www.maxlab.lu.se/positions and the links within this page, or from our Life-Sciences director Tomas Lundqvist . best regards Marjolein Thunnissen [cid:3A2194AC-734C-45EB-B5A7-CE7FC0F0F1BC] Marjolein Thunnissen Science Coordinator MX MAX IV Laboratory Lund University P.O. Box 118, SE-221 00 Lund, Sweden Visiting address: Ole Römers väg 1, 223 63 Lund Telephone: +46 766 32 04 17 www.maxlab.lu.se<http://www.maxlab.lu.se/>

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Integrated Structural Biology, PhD program at the IGBMC
by Alexandre OURJOUMTSEV 21 May '14

21 May '14

Dear all, kind reminder for PhD fellowship opportunities at the International PhD program of the IGBMC, notably for Integrated Structural Biology. Deadline for applications is 3rd of june 2014: http://phdprogramme.igbmc.fr/ Interested candidates are invited to visit the home pages of the teams of the Integrated Structural Biology department at http://www.igbmc.fr/research/department/3/ Please feel free to contact the group leaders for further information about the projects. Best regards, Bruno Klaholz Sacha Urzhumtsev

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any idea what is this? (unidentifiable blob in electron density map)
by Murpholino Peligro 21 May '14

21 May '14

1) 2FOFCWT PH2FOFCWT bue map (front1.png) (process: XDS->Aimless within CCP4i->MR with Phaser->Phenix.refine/coot->Phenix-refine-withwaters/coot) 2) FWT PHWT purple map (front2.png) (Output from Aimless and calculate Fs with refmac within coot with last pdb from 1st line) What do I have in the crystal? NaCl, Sodium acetate, water, lysozyme and some complexes (~ 400 daltons) that chelate Cu2+ Is there like a gallery of crazy-looking blobs that are explained with something ....real and possible? (that would be great help for the newb) Thanks in advance. links to screenshots right here: https://www.dropbox.com/s/rzjepvr8genolxi/front1.png https://www.dropbox.com/s/0iycf4lh5y726x4/front2.png https://www.dropbox.com/s/xx5kvgn91p763ei/faraway.png (1.0 rmsd for both maps above and 3.5 for the "red and green maps")

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phenix.rna_validate and the MolProbity web server report different bond angle violations
by Huw Jenkins 20 May '14

20 May '14

Hi, I’ve recently been using phenix.erraser to help correct RNA geometry errors and finding it very useful. However, it appears that the geometry validation statistics reported by phenix.rna_validate with respect to bond angle outliers are very different from those reported by the MolProbity web server. As an example - if I run phenix.rna_validate on 1u8d (as used in the documentation for phenix.erraser) the following outliers are reported: RNA Validation ----------------------------------------------- Pucker Outliers: #residue:delta_angle:is_delta_outlier:epsilon_angle:is_epsilon_outler G A 15 :74.054:no:103.458:yes U A 48 :119.081:yes:283.965:no U A 63 :90.366:yes:74.220:yes ----------------------------------------------- Bond Length Outliers: #residue:atom_1:atom_2:num_sigmas ----------------------------------------------- Angle Outliers: #residue:atom_1:atom_2:atom_3:num_sigmas C A 39 : C5': C4': C3':-5.294 U A 63 : O3': C3': C2':-4.402 ----------------------------------------------- Suite Outliers: #suiteID:suite:suiteness:triaged_angle G A 16 :!!:0.000:epsilon-1 U A 48 :!!:0.000:delta U A 49 :!!:0.000:delta-1 A A 64 :!!:0.000:epsilon-1 The MolProbity web server reports the same pucker and suite outliers but flags up many more angle violations: A 39 C worst is C5'-C4'-C3': 10.588 σ A 63 U worst is O3'-C3'-C2': 8.803 σ A 54 C worst is C5'-C4'-C3': 7.883 σ A 49 U worst is C2'-C1'-N1: 5.416 σ A 62 G worst is C2'-C1'-N9: 4.946 σ A 15 G worst is O3'-C3'-C2': 4.825 σ A 22 U worst is C5'-C4'-C3': 4.785 σ A 64 A worst is C4'-C3'-O3': 4.648 σ A 65 A worst is C2'-C1'-N9: 4.582 σ A 44 A worst is C4'-C3'-C2': 4.395 σ As the number of sigmas for the angle violations are different between phenix.rna_validate and MolProbity I guess they’re using different target distributions (not just reporting at a different sigma cut-off) but I’ve no idea which is more valid. Hopefully there is a simple explanation! Thanks, Huw

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Postdoctoral Fellow: Data Processing and Merging in Serial Crystallography
by Kay Diederichs 19 May '14

19 May '14

The Paul Scherrer Institute PSI is the largest research centre for natural and engineering sciences within Switzerland. We perform cutting-edge research in the fields of matter and materials, energy and environment and human health. By performing fundamental and applied research, we work on sustainable solutions for major challenges facing society, science and economy. PSI is committed to the training of future generations. Therefore about one quarter of our staff are post-docs, post-graduates or apprentices. Altogether PSI employs 1900 people. The Swiss Light Source (SLS) is one of the most advanced radiation sources worldwide. The SLS Macromolecular Crystallography Group operates two high performance undulator beamlines as well as a state-of-the-art bending magnet beamline for protein crystallography. The group is involved in several aspects of protein crystallography including the development of advanced beamline instrumentation and crystallographic methods, as well as structural biology projects in collaboration with the Biomolecular Research Group at PSI and external partners. In collaboration with Prof. Kay Diederichs at University of Konstanz, we are looking for a Postdoctoral Fellow: Data Processing and Merging in Serial Crystallography Your tasks ========== * Serial crystallography with bright micro-focused X-ray beams from both synchrotron and free electron laser sources has brought new opportunities in micro- and nanocrystallography. At the same time, obtaining best diffraction data from hundreds and thousands of crystals presents unprecedented challenges. New statistics based method of multi-crystal merging and analysis need to be developed and validated. * Develop multi-crystal data analysis, processing and merging methods for serial micro- and nanocrystallography at synchrotron radiation (SR) and X-ray free electron laser (XFEL) sources * Actively participate in serial crystallography experiments at both SR and XFEL sources * Implement an automated data merging pipeline at the SLS protein crystallography beamlines Your profile ============ You hold a PhD degree in (bio-)chemistry or physics and have several years of experience in protein crystallography. Working knowledge for data processing programs is a must. Experience in computer programming would be a significant advantage. If you are a good team player with good communication skills and sense of responsibility, this position will offer a great opportunity for you to develop your research career in an exciting and highly multidisciplinary environment. For further information please contact Prof. Kay Diederichs, phone +49 7531 88 40 49 or Dr Meitian Wang, phone +41 56 310 41 75. Please submit your application online (including list of publications and addresses of referees) for the position as a Postdoctoral Fellow (index no. 6112-00) to: Paul Scherrer Institute, Human Resources Management, Miriam Zehnder, 5232 Villigen PSI, Switzerland http://www.psi.ch/pa/offenestellen/0789-1 -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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Sharing a Phenix project via Dropbox
by Derek Logan 19 May '14

19 May '14

Hi, Has anyone ever successfully shared a Phenix project through Dropbox? I tried Googling for info on this without success. I have tried sharing but it doesn't work because Phenix uses the full path to the project, e.g. /Users/derek/Dropbox/project rather than ~/Dropbox/project, which would work for all users sharing the project. I tried manually editing project.phil in the .phenix directory, but at the end of a run of phenix.refine it was overwritten again. Is there somewhere (job_history.phil?) I can replace /Users/derek with ~ so that it the change will be permanent? I think that this would be a very effective way for me to set up a project being run by one of my PhD students involving people from at least 3 labs that could have opinions on the refinement! /Derek P.S. We are all using Macs.

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phenix.real_space_refine
by Gino Cingolani 15 May '14

15 May '14

Hi all, I'm trying to refine a pdb against an EM map using phenix.real_space_refine using default parameters (e.g. phenix.real_space_refine model1.pdb map.ccp4). The program starts OK but quickly stops with the following output (see below) Any thoughts? Thanks so much! Gino ########################################################################### Add C-beta restraints ********************* Adding C-beta torsion restraints... num c-beta restraints: 11832 ------------------------------------------------------------------------------- Getting target map ****************** Traceback (most recent call last): File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 494, in <module> o = run(sys.argv[1:]) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 273, in __init__ self.caller(func = self.get_target_map, prefix="Getting target map") File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 298, in caller func(prefix=prefix) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 372, in get_target_map number_of_macro_cycles = self.params.refinement.macro_cycles) File "/usr/local/phenix-dev-1615/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", line 153, in extract_target_map_data_and_crystal_gridding crystal_symmetry = inputs.xray_structure.crystal_symmetry()) File "/usr/local/phenix-dev-1615/cctbx_project/mmtbx/utils/__init__.py", line 3094, in structure_factors_from_map use_sg = True) File "/usr/local/phenix-dev-1615/cctbx_project/cctbx/miller/__init__.py", line 1309, in structure_factors_from_map assert map.focus_size_1d() > 0 and map.nd() == 3 and map.is_0_based() AssertionError ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu Website: http://www.cingolanilab.org ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) The information contained in this transmission contains privileged and confidential information. It is intended only for the use of the person named above. If you are not the intended recipient, you are hereby notified that any review, dissemination, distribution or duplication of this communication is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. CAUTION: Intended recipients should NOT use email communication for emergent or urgent health care matters.

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NCS in mr_rosetta
by Stefan Knight 15 May '14

15 May '14

Hi, Is there some way to make mr_rosetta use information about NCS present in the data? I have data from a crystal in sg P21 with a clear 3-fold axis perpendicular to the two-fold screw (as seen in self rotation function), and most likely 6 molecules in the asymmetric unit, but none of the mr_rosetta solutions that have appeared so far show 3-fold symmetry, and it doesn’t seem like the ncs is used in the search. The only info about ncs in mr_rosetta I have been able to find online pertains to extracting NCS from search models or mr_rosetta assembled models. Thanks, Stefan ------------------------------------------------------------------------------------------------------- Stefan D. Knight, PhD Professor of Biology Department of Cell and Molecular Biology, Uppsala University Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala Sweden Voice: +46 (0)18 471 45 54 Fax: +46 (0)18 53 03 96 E-mail: stefan(a)xray.bmc.uu.se ------------------------------------------------------------------------------------------------------- "We trained very hard, but it seemed that every time we were beginning to form into teams, we would be reorganised. I was to learn later in life that we tend to meet any new situation by reorganising - and a wonderful method it can be for creating the illusion of progress while producing confusion, inefficiency and demoralisation." – Gaius Petronius Arbiter (d. AD 66) -------------------------------------------------------------------------------------------------------

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