- phenixbb - phenix-online.org

AssertionError at asking for kicked maps
by Jorge Iulek 10 Apr '14

10 Apr '14

Dear all, It would be nice to have kicked maps for a structure I am working with now. When I set then to True, I get in my log: " ... shake map coefficients cycles: 0 1 2 3 4 5 6 7 8 9 shake f_model cycles: approx_equal eps: 1e-06 approx_equal multiplier: 10000000000.0 0.231506183818 approx_equal ERROR 0.235167389229 approx_equal ERROR Traceback (most recent call last): File "/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py", line 177, in run map_manger.write_files() File "/usr/local/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py", line 1780, in write_files map_coeff_dataset=self.write_mtz_file(), File "/usr/local/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py", line 1766, in write_mtz_file pdb_hierarchy=self.refine_object.model.pdb_hierarchy()) File "/usr/local/phenix-1.8.4-1496/cctbx_project/mmtbx/maps/__init__.py", line 515, in __init__ pdb_hierarchy = pdb_hierarchy) File "/usr/local/phenix-1.8.4-1496/cctbx_project/mmtbx/maps/__init__.py", line 439, in map_coefficients_from_fmodel map_type = params.map_type).map_coefficients File "/usr/local/phenix-1.8.4-1496/cctbx_project/mmtbx/maps/__init__.py", line 650, in __init__ assert approx_equal(fmodel.r_work(), fmodel_dc.r_work()) AssertionError " I see a previous problem like this at http://www.phenix-online.org/pipermail/phenixbb/2009-July/013517.html , but I cannot find a follow up concerning how to solve it. I am using the latest stable version, phenix-1.8.4-1496 , under openSuSE 12.3. When I set kicked maps to false, everything goes fine. Can this be solved? Also, a point to a former version that can "kick" would be enough. Thanks, Jorge

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fwd: Deadline is approaching: CCP4 crystallographic summer school in USA, at APS, June 24-July 2
by Nathaniel Echols 09 Apr '14

09 Apr '14

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Date: Tue, 8 Apr 2014 15:46:36 +0000 Subject: Deadline is approaching: CCP4 crystallographic summer school in USA, at APS, June 24-July 2 Dear Colleagues, We would like to remind you that the application deadline for the annual CCP4/APS Crystallographic Summer School in at the end of this week. The original announcement with some useful details is below. With best wishes, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ------------------------------ Dear Colleagues, We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2014/index.php *Title:*"CCP4 crystallographic school: From data collection to structure refinement and beyond" *Dates*: June 24 to July 2. *Site:* Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA *The school content: *Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 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 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.php<http://www.ccp4.ac.uk/schools/APS-2013/index.php> *Fees: *There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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GRC on Diffraction Methods: end July 2014
by Anastassis Perrakis 09 Apr '14

09 Apr '14

Dear all, We are getting closer and closer to the 2014 edition of my favorite Gordon Research Conference (https://www.grc.org/programs.aspx?year=2014&program=diffrac ) on Diffraction Methods in Structural Biology "Faster, Smaller, Better: Novel Technologies for Diffraction Experiments in Molecular Biology and Drug Discovery" , which this year will also feature before it starts the Gordon Research Seminars "Towards Integrative Structural Biology" (https://www.grc.org/programs.aspx?year=2014&program=grs_diff), targeting young scientists! Thanks to INSTRUCT (http://www.structuralbiology.eu) there will be four fellowships for young European researchers coming originally from an INSTRUCT member country or working in an INSTRUCT member country (http://www.structuralbiology.eu/resources/countries). Each fellowship will amount to 750 Euro, covering registration for both the GRC and the GRS, and all local expenses. It is a condition that you have to attend both the GRS and the GRC and submit a poster for both events. If you want to apply for such a fellowship, please send me an email reply (maintain the subject line please), including a single-page PDF file, a very short CV, an equally short abstract of your research, and a motivation statement explaining why you think this event is crucial for your career. Please include the email of your direct supervisor in the end of this letter, and a statement that she/he has agreed to cover the travel expenses for you to attend, if your fellowship application comes through. The deadline for receiving these letters is Wednesday 16 April at 12:CET (yes, thats less than a week from now! get writing!). The letters will be reviewed by an INSTRUCT panel, and the chosen four candidates will get a notification by the 8th of May! And, of course, I do take this opportunity to remind to everyone that the (almost) final program is on-line, we have an absolutely amazing group of speakers lined up, and the available places are filling up fast! So please remember to register on time! Looking forward to see you all at Bates College for what I trust you can make an exciting and memorable meeting! Best regards, Tassos PS If the file is not PDF, if its more than one page, if the characters you use are too small to read, etc etc, don't be too surprised if you do not get the travel fellowship award! Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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fix part of structure during refinement
by Jorge Iulek 08 Apr '14

08 Apr '14

Dear all, I want to test a refinement in which I fix part of my structure (say, residues 1 to 244 in chains C and D, and chains A and B completely) while the rest is to be refined with annealing. From the manual and http://www.phenix-online.org/pipermail/phenixbb/2009-June/013358.html, I have in my parameter file: " ... refine { strategy = *individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls *occupancies group_anomalous sites { individual = ( chain C and resseq 245:259 ) or ( chain D and resseq 245:259 ) torsion_angles = None rigid_body = None } ... " I thought atoms out of the selection in the output structure (chains A and B + residues 1 to 244 in chains C and D) would keep the same coordinates as they were input. But I see all structure atoms changed coordinates. I also tried to turn off tls and ncs usage, but the picture is the same. What do I miss here, to be able to fix some atoms during refinement? Thanks, Jorge

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Tenure track junior Group Leader positions at IEO, Milan, Italy
by Sebastiano Pasqualato 05 Apr '14

05 Apr '14

Dear all, please find enclosed the details to apply for junior Group Leader positions in Experimental and Computation Cancer Biology, open at the European Institute of Oncology, in Milan, Italy. -- Sebastiano Pasqualato, PhD Crystallography 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 web http://is.gd/IEO_XtalUnit -- Sebastiano Pasqualato, PhD Crystallography 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 web http://is.gd/IEO_XtalUnit

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calculating anomalous differences from a model
by Jonathan Grimes 05 Apr '14

05 Apr '14

Given a refined protein structure, is there an straightforward way to calculate the anomalous differences as a function of resolution, at wavelength X. many thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer DIAMOND Research Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: Jonathan(a)strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

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determining molprobity version?
by Pete Meyer 02 Apr '14

02 Apr '14

Hi, I may be missing something obvious, but how do I determine which version of molprobity is being used for generating the clash scores reported by phenix.model_vs_data ? Pete

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error estimates on coordinates
by Benoît Masquida 28 Mar '14

28 Mar '14

Hello, Can someone shed light on the way coordinates errors are obtained in REMARK 3 using maximum of likelihood as compared to Luzzati or sigmaa? What article can be cited in this respect? Thanks in advance. Benoit -- Benoît Masquida Chargé de Recherche CNRS GMGM, UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB, 21, rue René Descartes 67084 Strasbourg b.masquida(a)unistra.fr

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phenix.pdbtools model_statics=true
by Maehigashi, Tatsuya 27 Mar '14

27 Mar '14

Hi all, What would be the best way to define the "selection" to show average B factors using phenix.pdbtools from command line? I've tried several ways using something like... phenix.pdbtools XXXXX.pdb stop_for_unknown=false model_statistics=true selections="chain QA or chain RA" However, the output always contain the standard/default "ADP statistics" table only (not for the selection I specified). Yes, I'm aware of the GUI option (under other tools) and it works great. However, I'm trying to compute average b for 9 coordinates under 4 separate categories (protein, RNA, ligands... and such), and I think it'll be a lot easier from the command line (using some quick script, for example). Any input will be appreciated! "T" ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Obtaining just the Wilson B with Xtriage
by Morten Grøftehauge 27 Mar '14

27 Mar '14

Hi guys, Is there a way to just have phenix.xtriage compute and output the Wilson B factor and not do everything else? I want to run it on a lot of files and that would simplify things. Cheers Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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