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Not a suitable array of R-free flags:
by Yamei Yu 26 Nov '14

26 Nov '14

Dear all, I use phenix.refine to refine a structure. Firstly, I used --dryrun to generate an .eff file. The command is "phenix.refine --dry_run 7_44.mtz 7_44.pdb refinement.input.xray_data.r_free_flags.generate=True refinement.input.xray_data.r_free_flags.max_free=1000” Then I use run the program by typing “phenix.refine 7_44_refine_001.eff” It runs correct! After that I use coot to modulate some parts of the structure, then I want to refine the structure again. I type “ phenix.refine 7_44_refine_002.def” This time I got the following error message: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=R-free-flags Sorry_Not_a_suitable_array: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=R-free-flags To override the suitability test define: refinement.input.xray_data.r_free_flags.disable_suitability_test=True I checked the generated file by phenix “7_44_refine_data.mtz” I does contain a column labeled as R-free-flags. I paste part if it below. * Space group = 'P1' (number 1) OVERALL FILE STATISTICS for resolution range 0.000 - 0.277 ======================= Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 ASC -32 31 0 100.00 -2.2 11.9 49.44 1.90 H H 2 NONE -46 45 0 100.00 -2.5 17.8 49.44 1.90 H K 3 NONE 0 49 0 100.00 18.8 18.8 49.44 1.90 H L 4 NONE 0.9 271.3 0 100.00 26.52 26.52 49.44 1.90 F F-obs 5 NONE 0.2 5.1 0 100.00 1.25 1.25 49.44 1.90 Q SIGF-obs 6 NONE 0.0 1.0 0 100.00 0.01 0.01 49.44 1.90 I R-free-flags No. of reflections used in FILE STATISTICS 143215 Then I regenerate a new mtz file with FreeRflag by XDSCONT, then I revise the .def file accordingly and rerun the program. I got same error message:Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=FreeRflag Sorry_Not_a_suitable_array: Not a suitable array of R-free flags: refinement.input.xray_data.r_free_flags.label=FreeRflag To override the suitability test define: refinement.input.xray_data.r_free_flags.disable_suitability_test=True I checked my new mtz file, it dose contain a column labeled as FreeRflag Why there is an error message? How to solve it? Thank you so much!! Best wishes! yamei ************************************************ Yamei Yu State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyuxtal(a)gmail.com ymyuxtal(a)163.com yamei_yu(a)scu.edu.cn

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error messages running phenix.mr_rosetta
by Ursula Schulze-Gahmen 26 Nov '14

26 Nov '14

I am running mr_rosetta on a 64bit Linux computer. The model optimization worked without a problem, but now in the molecular replacement step I am receiving error messages, and I am not sure what the problem is. Could anyone provide a suggestion? Thanks Ursula /usr/share/themes/Slider/gtk-2.0/gtkrc:80: error: unexpected identifier `colorize_scrollbar', expected character `}' Fontconfig warning: no <cachedir> elements found. Check configuration. Fontconfig warning: adding <cachedir>/var/cache/fontconfig</cachedir> Fontconfig warning: adding <cachedir>~/.fontconfig</cachedir> (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): Pango-WARNING **: Failed to load Pango module '/programs/x86_64-linux/phenix/dev-1819/phenix-dev-1819/build/intel-linux-2.6-x86_64/base/lib/pango/1.6.0/modules/pango-basic-fc.so' for id 'BasicScriptEngineFc' (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): GLib-GObject-WARNING **: Two different plugins tried to register 'BasicEngineFc'. (gedit:20211): GLib-GObject-CRITICAL **: g_object_new: assertion `G_TYPE_IS_OBJECT (object_type)' failed (gedit:20211): Gtk-WARNING **: Could not find the icon 'system-file-manager'. The 'hicolor' theme was not found either, perhaps you need to install it. You can get a copy from: http://icon-theme.freedesktop.org/releases -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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residue selection for rsrl?
by Kevin Jude 26 Nov '14

26 Nov '14

I am refining a structure at 2.9 Å resolution and have two side chains that keep moving out of density during reciprocal space refinement; both side chains should fit the resulting Fo-Fc density in favored rotamers. Turning on real-space refinement fixes this problem but leads to higher Rfree and poorer geometry overall. Can I select a subset of residues for real space refinement while still performing reciprocal space refinement on the whole asymmetric unit? Thanks for any help Kevin

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phenix rosetta refine
by Andreas Förster 26 Nov '14

26 Nov '14

Dear all, I'm trying to get phenix.rosetta_refine to run. I think it's all set up properly, with Rosetta 3.5 and Phenix 1810 on RHEL 6.3 64bit. However phenix.rosetta_refine model.pdb data.mtz nproc=48 protocol=full > log& fails with the following error in log: End of input processing Sorry: The RosettaScripts executable could not be located. Please add the appropriate directory to your PATH environment variable, or set the variable ROSETTA_BIN to point to it. To me it seems things are defined correctly: andreas@csbstereo in phenix: echo $ROSETTA_BIN /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin andreas@csbstereo in phenix: ls $ROSETTA_BIN | grep scripts rosetta_scripts.linuxgccrelease@ rosetta_scripts.default.linuxgccrelease@ andreas@csbstereo in phenix: ll $ROSETTA_BIN/rosetta_scripts.linuxgccrelease lrwxrwxrwx 1 csbadmin csb 93 Oct 9 2013 /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -> ../build/src/release/linux/2.6/64/x86/gcc/4.4/default/rosetta_scripts.default.linuxgccrelease Any idea of what's wrong would be greatly appreciated. Andreas -- Andreas Förster X-ray Crystallography Facility Manager Centre for Structural Biology Imperial College London

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Alternative conformation of ligand with near zero occupancy
by Singh, Bishal 26 Nov '14

26 Nov '14

Hello everybody, I thank you for clarifying my previous doubts. Your suggestions matter a lot to me. Here I have another doubt. I have structure of a protein in complex with triglycan (fucose-galactose-galactose). The terminal galactose of this triglycan possesses two conformations with occupancies 0.4 and 0.6. In order to satisfy the geometric parameters of this triglycan, I derived the alternative conformation of fucose and the central galactose as well. Then I performed occupancy refinement. The occupancy of alternative central galactose is 0.06 and that of alternative fucose is 0.00. Now the question is, should I delete this fucose of zero occupancy or keep it to maintain the geometric parameters of triglycan? I am looking forward for your opinion. If you like I can provide a snapshot of ligand with electron density. With regards, Bishal Singh PhD student DKFZ, University of Heidelberg, Germany

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input for specifying labin in phenix.find_ncs
by Arka Chakraborty 26 Nov '14

26 Nov '14

Dear Phenix BBers, I have a seemingly trivial problem in specifying column labels in phenix.find_ncs. Following the manual, on entering labels as : phenix.find_ncs xx.pdb yy.mtz params.ncs.labin = "labin FP=F PHIB=PHI FOM=FOM" , phenix returns the error : 'Sorry, cannot interpret the keyword: params.ncs.labin=labin FP=F PHIB=PHI FOM=FOM'. Any clues on what mistake I might be making will be greatly appreciated. Thanks a lot, Regards, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*

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Different space group of coordinate and structure factors
by Singh, Bishal 25 Nov '14

25 Nov '14

Hello everybody, For a data-set, the space group after data-processing was P4222. When I performed molecular replacement through PHASER in phenix keeping the search option 'All possible in same point group", the space group changed to P41212. Now the question is that shall I process the data again in this new space group or should I move on for refinement? Please suggest me your opinion. With regards, Bishal Singh PhD Student DKFZ, University of Heidelberg, Germany

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explicit solvent in low resolution refinement
by Guenter Fritz 25 Nov '14

25 Nov '14

Dear all, we have determined the structure of a protein complex at 3.5 A resolution as well as the structures of three subunits of this complex independently at resolutions better than 2 A. I had used the models of the subunits as reference models in refinement, perfect. Now I was wondering whether one could use explicit solvent positions (e.g. inner shell water molecules) from the high resolution structures in the low resolution refinement. This should be superior to a simple bulk solvent model. I placed the inner shell water molecules from the high res structures into the low res model and added harmonic restraints to the water positions in low res refinement. I see a decrease of about 0.5% in Rwork and Rfree versus the model without water molecules. However, adding harmonic restraints excludes the option to use the reference models in refinement. Is it possible to use protein and water atoms from the reference models to generate restraints for the low resolution refinement? Thank you, Guenter

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ready set and H/D addition on waters
by Maxime Cuypers 24 Nov '14

24 Nov '14

hello, after not using phenix for a while, i just realised the new versions do not include the option in ready_set gui to add H or D atoms to waters in the pdb models (and only to the waters without altering the rest of the model would be nice). of course it can be done on the command line but why has it been removed? it is a very neutron crystallographer friendly option don t you think? cheerios, -- Dr. Maxime Cuypers

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Rwork > Rfree
by Singh, Bishal 21 Nov '14

21 Nov '14

Hello everybody, While depositing a structure in PDB, I observed that Rwork was more than Rfree in the highest resolution shell and in a few more shells as well. I shall be delighted if somebody can suggest me the reasons and also what should I do now. With regards, Bishal PhD student, DKFZ, University of Heidelberg, Germany

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