- phenixbb - phenix-online.org

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 23 Jan '13

23 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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Still can't get refinement of anomalous groups to work
by Brennan Bonnet 16 Jan '13

16 Jan '13

Hi all, I'm still working on this pesky anomalous group refinement problem. Originally, the problem was that the output from AutoBuild no longer retained the anomalous data. To fix this, I used the Phenix reflection file editor and combined exptl_fobs_phases_freeR_flags.mtz (which is automatically entered as input when running phenix.refine from AutoBuild) with the F+ F- values from my original reflection data. Now when I try to run refinement I get this error message: "This model appears to have previously been refined against a different set of R-free flags. Please resolve the mismatch." I find this strange since I am only modifying the file that phenix.refine tries to use anyway. How do I fix this problem? Thanks, ~Brennan~

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