January 2013 - phenixbb - phenix-online.org

RapiData: Seats are available - the deadline is in 10 days for our course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 25 Jan '13

25 Jan '13

We will present RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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B-factor calculation
by Wei Shi 24 Jan '13

24 Jan '13

Hi guys, I am wondering how I can calculate average B-factor in phenix GUI. I read from an old post saying that, the following will give me complete statistics about B-factors, but in pdbtools in phenix GUI, I didn't find how to show adp statistics. phenix.pbdtools your_model.pdb --show-adp-statistics Besides, I am wondering how I can find the B-factor for each residue and plot the variation of B-factor by residue. Thank you so much! Best, Wei

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phenix.refine crash due to MTZ input
by wtempel 24 Jan '13

24 Jan '13

Hello, this may perhaps fall under "garbage in, garbage out". The following reflection results in the appended stack trace. Would it be reasonable to instead just treat such reflection as missing? Best regards, Wolfram Tempel <mtz.dmp> RFREE F_r1lo1 SIGF_r1lo1 DANO_r1lo1 SIGDANO_r1lo1 F_r1lo1(+) SIGF_r1lo1(+) F_r1lo1(-) SIGF_r1lo1(-) ISYM_r1lo1 IMEAN_r1lo1 SIGIMEAN_r1lo1 I_r1lo1(+) SIGI_r1lo1(+) I_r1lo1(-) SIGI_r1lo1(-) 20 4 54 11 None None -3.61389 15.223 19.349 9.78972 22.9629 11.6577 0 -227.641 69.6184 -205.607 83.633 -277.365 125.635 </mtz.dmp> <trace> Traceback (most recent call last): File "Blah/phenix-1.8-1069/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 "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 74, in run master_params=customized_master_params) File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 274, in __init__ reflection_file_server = self.reflection_file_server() File "Blah/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 793, in reflection_file_server err=self.log) File "Blah/phenix-1.8-1069/cctbx_project/iotbx/reflection_file_utils.py", line 448, in __init__ force_symmetry=self.force_symmetry)) File "Blah/phenix-1.8-1069/cctbx_project/iotbx/reflection_file_reader.py", line 209, in as_miller_arrays base_array_info=base_array_info) File "Blah/phenix-1.8-1069/cctbx_project/iotbx/mtz/__init__.py", line 502, in as_miller_arrays dataset=dataset) File "Blah/phenix-1.8-1069/cctbx_project/iotbx/mtz/__init__.py", line 610, in group_columns group = self.extract_delta_anomalous(*labels) RuntimeError: cctbx Error: Invalid combination of values while extracting anomalous array from columns: F_r1lo1, SIGF_r1lo1, DANO_r1lo1, SIGDANO_r1lo1, hkl=(20,4,54) [tip: "phenix.mtz.dump --show_column_data file_name" is available for inspecting the MTZ file] </trace>

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Re: [phenixbb] Phenix for Ubuntu 12.04
by Kay Diederichs 23 Jan '13

23 Jan '13

Hi Eugene, Nat, apt-get install libjpeg62 was indeed useful. After installing that, the GUI starts but I get the error AssertionError : Traceback (most recent call last): File "/usr/local/phenix/phenix-dev-1269/build/intel-linux-2.6-x86_64/../../phenix/wxGUI2/command_line/main.py", line 22, in <module> run(sys.argv[1:]) File "/usr/local/phenix/phenix-dev-1269/build/intel-linux-2.6-x86_64/../../phenix/wxGUI2/command_line/main.py", line 17, in run wxapp = App.PhenixApp(args) File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/App.py", line 58, in __init__ wx.App.__init__(self, 0) File "/usr/local/phenix/phenix-dev-1269/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 7981, in __init__ self._BootstrapApp() File "/usr/local/phenix/phenix-dev-1269/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 7555, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/App.py", line 101, in OnInit self.start_gui() File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/App.py", line 174, in start_gui self.launch_main() File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/App.py", line 453, in launch_main frame = PhenixGUI() File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/Home/Main.py", line 37, in __init__ wx.CAPTION | wx.CLIP_CHILDREN) File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/MainWindow.py", line 229, in __init__ PhenixFrameBase.__init__(self, parent) File "/usr/local/phenix/phenix-dev-1269/phenix/wxGUI2/MainWindow.py", line 36, in __init__ assert self.project is not None AssertionError -- 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 647, D-78457 Konstanz

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Phenix for Ubuntu 12.04
by Kay Diederichs 23 Jan '13

23 Jan '13

Dear all, coming from RedHat Linux, I have a difficult time to install the latest nightly phenix build on a 64bit Ubuntu 12.04 LTS notebook. (I must confess that I did not try any older or stable releases, like 1.8.1) The reason why I did not install SL6 on the notebook is that it comes with Windows installed on fake RAID. Since I don't want to get rid of Windows completely, and thus can only take half of the disk for Linux, I wanted to use Ubuntu which offers an alternate installer supporting fake RAID. I tried the FC3 binary installer (which is offered by default), as well as the FC8 FC12 FC14 installers. Installation works, but upon startup libjpeg.so.62 is missing (libjpeg.so.80 is installed but they are incompatible). So I tried the source installer, but that fails with ERROR: installation of xrender failed ERROR: installation of xft failed ERROR: installation of cairo failed ERROR: installation of pango failed ERROR: installation of gtk failed ERROR: installation of gtk-engine failed ERROR: installation of wxgtk failed ERROR: installation of wxpython failed So I believe I should apt-get install certain packages. Does anyone know which ones? thanks, Kay -- 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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Problems with occupancy summation when more than two alt. conf.
by Haim Rozenberg 23 Jan '13

23 Jan '13

Hello, It seems that after "refine", the summation of occupancies is not always equal to 1.00 when more than two alternative conformations are defined in the pdb. In recently refined structures we were surprise to find 1.01 instead of 1.00 (Big deal ??? Yes, for the deposition/validation!). We didn't find any warning nor error messages in the corresponding log files. (phenix.refine: 1.8.1_1168) or newer, on Mac as well as Linux machines. Best regards, Haim ============================================ Haim Rozenberg, PhD. Department of Structural Biology Kimmelman Building Weizmann Institute of Science 76100 Rehovot, Israel Phone: +972-8-9344289 FAX:+972-8-9344136 E-Mail: haim.rozenberg(a)weizmann.ac.il ============================================ "Quis custodiet ipsos custodes?" D.I. Iuvenalis

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structure factors for PDB deposition
by wtempel 22 Jan '13

22 Jan '13

Hello all, based on ${prefix}_001_f_model.mtz from phenix.refine, I would like to prepare a cif file with structure factors. FOBS, SIGFOBS, R_FREE_FLAGS, FMODEL, PHIFMODEL, FOM are available in (+) and (-) versions, presumably representing Bijvoet pairs. My questions are: 1) are FMODEL, PHIFMODEL the most appropriate columns for calculated amplitudes and phases for the purpose of PDB deposition? 2) I understand that the PDB sf_tool does not accommodate separate (+)/(-) columns for some of the items. A job for phenix.reciprocal_space_arrays and a reflection file without anomalous differences? Alternatively, I imagine that phenix has a tailored procedure just for the preparation of PDB deposition, but I may not have used the correct web search terms to find the instructions. Thank you in anticipation, Wolfram Tempel

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fwd: WCPCW 21 - registration deadline!
by Nathaniel Echols 21 Jan '13

21 Jan '13

---------- Forwarded message ---------- From: "Williams, John Charles" <jwilliams(a)coh.org> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Cc: Date: Mon, 21 Jan 2013 11:16:14 -0800 Subject: WCPCW 21 - registration deadline! Dear All, Today is technically the last day of standard registration rates. I have had a couple of emails this morning asking for extra time (approval by business manager, etc.). To accommodate everyone, we will extend the rate standard rates until Wednesday, Jan 23rd. Also, please submit your abstract soon. We have a significant number of people already registered and will have have to select abstracts for oral presentations. Best, John

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Structure minimization for model with rigid body
by danashah＠post.tau.ac.il 18 Jan '13

18 Jan '13

Hi all, We're interesting in performing a structure minimization for a model, while treating a part of the model as a rigid body. Is there an option for that on PDB tools via geometry minimization? Or is there another way to do that? Thank you, Dana. __ Dana Sachyani Joel Hirsch's Lab Faculty of Life Sciences Tel Aviv University Ramat Aviv, Israel e-mail: danashah(a)post.tau.ac.il

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Bug squash request
by Antony Oliver 17 Jan '13

17 Jan '13

Dear Phenix-developers, I've noticed a slightly annoying "feature" when using a reference model to help in refinement of low-resolution structures. phenix.refine seems to take it's crystal parameters and space-group from whichever PDB was loaded last, even after setting one PDB as the "reference model" and the other as the "Input model". When running phenix.refine it gives you a nice error message telling you that the space group information is incorrect, and that you may have used the reference model's parameters by mistake… But surely, it should just (by default) only take (check?) the cell parameters and space group information from the "Input PDB"? With thanks, Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512

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