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Re: [phenixbb] problem in rosetta rebuilding
by intekhab alam 01 Aug '11

01 Aug '11

Hi, Tom sorry for the delayed response. I was abale to fix by running one model. rosetta is working fine now. thanks again Intekhab Alam On Thu, Jul 21, 2011 at 11:49 PM, Thomas C. Terwilliger < terwilliger(a)lanl.gov> wrote: > Hi Intekhab, > > I'm glad the test works at least. How about trying this: > > Run just the job that hangs, but instead of running 100 models...just run > one single model. Does that work? > > All the best, > Tom > > > >> Hi Tom > >> i tried the commnad line and it works well. we also have increased the > >> memory to 3GB (earlier it was 2GB) > >> but still the system hangs with no response overnight. > >> the specifications of my system is as: > >> Ubuntu 9.04 > >> GCC 4.2 > >> RAM 3GB > >> Rosetta 3.2 > >> Phenix 1.7.1 > >> the command line test using > >> "phenix_regression.wizards.test_command_line_rosetta_quick_tests > >> test_rosetta_rebuild" works well . > >> > >> regards > >> intekhab alam > >> On Tue, Jul 19, 2011 at 11:31 PM, Thomas C. Terwilliger < > >> terwilliger(a)lanl.gov> wrote: > >> > >>> Hi Intekhab, > >>> > >>> I'm not sure about the part about the machine shutting down...but here > >>> is > >>> a little test you can run to make sure that rosetta and phenix are > >>> working > >>> properly together in rebuilding a model: > >>> > >>> phenix_regression.wizards.test_command_line_rosetta_quick_tests > >>> test_rosetta_rebuild > >>> > >>> or a more complete set of tests: > >>> > >>> phenix_regression.wizards.test_command_line_rosetta_quick_tests > >>> > >>> All the best, > >>> Tom T > >>> > >>> > >>> > >>> >> On 07/19/2011 04:49 PM, intekhab alam wrote: > >>> >>> > >>> >>> Hi > >>> >>> i tried to run rosetta on a unix machine (ubuntu 9.04) for my data. > >>> Upto > >>> >>> MR step everything goes fine , but during the rebuilding step after > >>> 20 > >>> >>> cycles the computer shuts down. > >>> >> > >>> >> Interesting behavior for a Linux machine. > >>> >> > >>> >> Once the machine has rebooted, reading the output > >>> >> of the dmesg command and looking at events prior to the last boot > >>> >> may give you some information on why the computer hung. > >>> >> > >>> >> My guess is that you went out of memory while using mr_rosetta. > >>> >> > >>> >>> i have attached the log file for the autobuilding run of rosetta. i > >>> am > >>> >>> using phenix 1.7.1-743 version. > >>> >>> i will be grateful if some one helps me out > >>> >>> -- > >>> >>> INTEKHAB ALAM > >>> >>> LABORATORY OF STRUCTURAL BIOINFORMATICS > >>> >>> KOREA UNIVERSITY, SEOUL > >>> >>> > >>> >>> > >>> >>> > >>> >>> _______________________________________________ > >>> >>> phenixbb mailing list > >>> >>> phenixbb(a)phenix-online.org > >>> >>> http://phenix-online.org/mailman/listinfo/phenixbb > >>> >> > >>> >> _______________________________________________ > >>> >> phenixbb mailing list > >>> >> phenixbb(a)phenix-online.org > >>> >> http://phenix-online.org/mailman/listinfo/phenixbb > >>> >> > >>> > >>> _______________________________________________ > >>> phenixbb mailing list > >>> phenixbb(a)phenix-online.org > >>> http://phenix-online.org/mailman/listinfo/phenixbb > >>> > >> > >> > >> > >> -- > >> INTEKHAB ALAM > >> LABORATORY OF STRUCTURAL BIOINFORMATICS > >> KOREA UNIVERSITY, SEOUL > >> > > -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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I seem to be unable to select the map_coeff_labels for phenix.cut_out_density
by Pietro Roversi 31 Jul '11

31 Jul '11

Dear Tom I am trying to run phenix.cut_out_density but I seem to be unable to select the map_coeff_labels: viscount:~/sharpfiles/logfiles/Japanin-ID29-Phaser714.15> phenix.cut_out_density cycle_best_13.pdb eden_flat_55.0pc.mtz << EOF map_coeff_labels="FBshasol SIGFPsha PHIBshasol FOMshasol" EOF The output (see below) says I did not give SIGFP and it also picks the default F,PHI and FOM from columns 4,5,6 What am I doing wrong? Thanks! Pietro # cutout # # Cut out density from a map # Type phenix.doc for help Cutting out density Miller arrays in mtz_in: ['H', 'K', 'L', 'Fcentsha', 'PHIcentsha', 'FOMsha', 'HLA', 'HLB', 'HLC', 'HLD', 'FHsha', 'PHIHsha', 'FreeR_flag', 'FPsha', 'SIGFPsha', 'Fcentshasol', 'PHIcentshasol', 'FBshasol', 'PHIBshasol', 'PHIshasol', 'FOMshasol', 'HLAshasol', 'HLBshasol', 'HLCshasol', 'HLDshasol', 'FCshasol', 'PHICshasol'] Setting FP and PHI from map_coeffs Setting FP and PHI from map_coeffs Setting FP and PHI from map_coeffs Setting FP and PHI from map_coeffs Setting FP and PHI from map_coeffs Center of cutout region will be from model center at: [62.32560090909093, 43.68719545454543, 32.72059636363636] ------------------------ COPYRIGHT NOTICE --------------------------------- Los Alamos National Laboratory This program was prepared by Los Alamos National Security, LLC at Los Alamos National Laboratory (the University) under Contract No. W-7405-ENG-36 with the U.S. Department of Energy (DOE). The University has certain rights in the program pursuant to the contract and the program should not be copied or distributed outside your organization. All rights in the program are reserved by the DOE and the University. Neither the U.S. Government nor the University makes any warranty, express or implied, or assumes any liability or responsibility for the use of this software. ******************************************************* * --- RESOLVE --- * * * * Statistical density modification * * Automated model-building * * * * For on-line help * * see "http://solve.lanl.gov" * * * * This software uses library routines from the * * CCP4 suite (http://www.ccp4.ac.uk) for which * * the author is very thankful! * ******************************************************* (version 2.15 of 20-Mar-2010) (size = 6) Tom Terwilliger, Los Alamos National Laboratory, "terwilliger(a)LANL.gov" >pdb_in_memory Reading pdb_in from memory If "no_reuse_model" is not set then this model will also be used as starting point for model-building >no_build Model will not be built >mask_cycles 1 Number of mask/image cycles: 1 >minor_cycles 0 Number of minor cycles per mask/image cycle: 0 >no_build Model will not be built >cutout Cutting out density near cutout_center and writing to P1 cell >fine_grid FFT grid will be extra fine (1/5 of resolution) >no_sort The atoms in pdb_in will not be sorted. >resolution 1000 2.13352593412 Resolution range (A) is: 2.133526 to 1000.000 >cell1 15.0 15.0 15.0 90 90 90 Cell for cutout (cell1) is 15.00000 15.00000 15.00000 90.00000 90.00000 90.00000 >cutout_center 62.3256009091 43.6871954545 32.7205963636 Center of density for cutout (cutout_center) is 62.32560 43.68719 32.72060 >padding 5.0 Padding around cutout of density: 5 A >cutout_mask 1 Cutout mask type (1=box, 2=sphere, 3=mask around model): 1 >cutout_sphere 10.0 Radius of cutout of density around cutout_center: 10 A >rad_mask 5.0 Radius for creating solvent model: 5.000000 > All done with inputs Not writing any files as information returned in memory Building protein Setting up for building protein Standard fill-in residues: ALA A GLY G Standard main-chain atoms: N CA C O CB All main-chain atoms: N CA C O Max dist between adjacent N atoms: 6.000000 List of all residues: GLY ALA SER VAL ILE LEU MET CYS PHE TYR LYS ARG TRP HIS GLU ASP GLN ASN PRO THR List of 1-letter code of residues: GASVILMCFYKRWHEDQNPT List of number of atoms in side-chains: 0 1 2 3 4 4 4 2 7 8 5 7 10 6 5 4 5 4 3 3 checking license file.. solve2.access The date today is 31-jul-11. Your license is good until 15-dec-96. Space group name: Point group: Space group number : 96 Symmetry operators: 8 Done with lookup FP taken from column 4 No dataset found matching ID = 0 PHIB taken from column 5 FOM taken from column 6 Using HLA HLB HLC HLD coefficients WARNING: No SIGFP input data--output SIGFP column will be SIGFP=1.0 for all HKL! Reading in FreeR_flag Total of 5695 reflections read from file Guessing FreeR_flag corresponding to free reflections This can be set with free_id xx Free R reflections are those with FreeR_flag= 0 Total of 251 of 5695 reflections in test set High-resolution limit of input phased data: 3.21 Adding F000 term (0.0) to this list Closed mtz file Starting resolution: 3.20 max: 3.20 Space group is 96 Using symmetry operations from input MTZ file MATRICES: SYMMETRY ELEMENT 0 1 0 0 0 0 1 0 0 0 0 1 0 SYMMETRY ELEMENT 1 0 -1 0 0.5 1 0 0 0.5 0 0 1 0.75 SYMMETRY ELEMENT 2 0 1 0 0.5 -1 0 0 0.5 0 0 1 0.25 SYMMETRY ELEMENT 3 1 0 0 0.5 0 -1 0 0.5 0 0 -1 0.25 SYMMETRY ELEMENT 4 -1 0 0 0.5 0 1 0 0.5 0 0 -1 0.75 SYMMETRY ELEMENT 5 -1 0 0 0 0 -1 0 0 0 0 1 0.5 SYMMETRY ELEMENT 6 0 1 0 0 1 0 0 0 0 0 -1 0 SYMMETRY ELEMENT 7 0 -1 0 0 -1 0 0 0 0 0 -1 0.5 SPACE GROUP SYMBOL: P 43 21 2 CHECK ON SPACE GROUP SYMBOL: P 43 21 2 HALL SYMBOL : P 4nw 2abw Extra fine grids used for FFT Transformations from orthogonal to fractional and back: Orthogonal to fractional fractional x= 0.01183 X + -0.00000 Y + -0.00000 Z fractional y= 0.00000 X + 0.01183 Y + -0.00000 Z fractional z= 0.00000 X + 0.00000 Y + 0.01123 Z Fractional to orthogonal Orthogonal X= 84.50000 x + 0.00010 y + 0.00010 z Orthogonal Y= 0.00000 x + 84.50000 y + 0.00010 z Orthogonal Z= 0.00000 x + 0.00000 y + 89.05000 z Estimated # of atoms in au: 2510 Not separating out FREE set from other reflections for main cycles. Using all data. Results of wilson scaling: Scale on I = 3.274 B-value = 47.194 Scaling data with value of 3.274 Reading model density histograms from /software/xtal/PHENIX/phenix-1.7.1-743/solve_resolve/ext_ref_files/segments/rho.list Read total of 6 sets of density functions Highest value of ix, iy, iz in a.u: 143 143 18 nu nv nw: 144 144 144 Number of grid points in au: 373320 Mean fom of this map was: 0.84 Summary of starting FOM vs resolution RES FOM FOM-smoothed N 29.25 0.89 0.86 27 17.82 0.79 0.86 42 13.27 0.71 0.86 72 10.48 0.85 0.86 120 8.83 0.89 0.85 118 7.63 0.84 0.85 206 6.65 0.85 0.85 243 5.96 0.88 0.85 268 5.43 0.85 0.85 306 5.03 0.88 0.85 313 4.67 0.89 0.85 415 4.38 0.86 0.84 348 4.15 0.88 0.84 445 3.91 0.86 0.84 567 3.67 0.84 0.84 701 3.46 0.82 0.84 675 3.28 0.78 0.83 829 Mean fom of this map was: 0.84 Starting phases assumed to be experimental (To override, use "phases_from_resolve") Estimating optimal initial smoothing radius using the function: R=2.41 * (dmin**0.90) * (fom**-0.26) with dmin = 3.200273 and fom = 0.8443282 Leading to R= 7.174512 To override, set "wang_radius_cycle", "wang_radius", or "wang_radius_start" Setting final smoothing radius to 4.000000 To override, set "wang_radius_cycle", "wang_radius", or "wang_radius_finish" Using pdb_in from memory Center of molecule read in with 1081 atoms is 62.275337 43.672276 32.612022 Read 1081 atoms from PDB file for use in model-building MEMORY Solvent content will be 0.40 Using database entry 5 for histograms (" 3 A dehalogenase model ") Using all data for tests due to low number in test set (override with "use_free_for_test") Total mask cycles: 1 Total density modification mask cycles: 1 Cycle Ref NCS Use NCS Build image solvent Extend Cycles Test 1 NO NO NO NO YES NO 0 Mask cycle 1 Weighting this cycle: 1.000000 Histogram DB entry # 5 (" 3 A dehalogenase model ") Solvent content: 0.40 Smoothing radius: 7.17 Using histogram-based mask Assuming this cycle is unbiased (no previous density modification) Plot 1 ------------------------------------------------------------------------------- Plot of probability that a grid point is part of protein region vs percentiles of grid points All points to the left of the "+" signs are in solvent masked region those to right are in protein masked region. The values of p(protein) should change from low to high approximately at the value of the fraction of solvent indicated by the "+" signs. The sharper the transition the better. Note: the mask is only used to make an estimate of the p(protein) The values of p(protein) are used to weight the contribution of each grid point to the probability of the map: p(rho) = p(rho|protein) p(protein) + p(rho|solvent) (1-p(protein)) This says that the probability that we would observe the value "rho" of electron density at this point is the probability that we would observe "rho" if this were really protein times the probability that this is protein, plus the probability that we would observe "rho" if it were really solvent, times the probability that it is solvent. Probability that grid points are in protein region 1.0 ...........................xxxxxxxxxxxxxxxxxxxxxxx . + xx . . + x . . + x . . + . . + x . . + . p(protein) . xxxxxx . 0.5 . xxxxxxxxxxxxx + . . + . . x + . . + . .x + . . + . . + . 0.0 ....................+............................. 0 20 40 60 80 100 Percentile of grid points ------------------------------------------------------------------------------- Cutting region containing model out of map Box to be cut out of density (A) : 15 15 15 Box with padding (A) : 25 25 25 NX NY NZ for cutout box: 36 36 36 NX NY NZ with padding: 60 60 60 Center of cutout region (A): 62.3256 43.6872 32.7206 Using box for cutout mask Total grid points marked: 46656 not marked: 169344 Mean density in cutout region (no density offset applied ) 0.040 for 46656 points Number of points in padded region (set to 0.0): 169344 Output array in memory with 3600 reflections resolve exit_info: source_file: /net/longnose/scratch2/phenix/phenix-1.7.1-743/solve_resolve/resolve/cutout.cpp source_line: 252 status: 0 EndOfResolve Output map coeffs 3600 Writing output mtz: cutout.mtz Writing output pdb (offset to match output mtz): cutout.pdb Citations for cutout: Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D66:213-221. ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] On Behalf Of Thomas C. Terwilliger [terwilliger(a)lanl.gov] Sent: 05 July 2011 17:46 To: PHENIX user mailing list Subject: Re: [phenixbb] phenix.mr_rosetta: Inconsistent query numbering Hi Pietro, There is something that phenix.mr_model_preparation cannot read in Japanin.hhr (attached): phenix.mr_model_preparation Japanin.hhr gives the same error. I'll copy Gabor Bunkoczi and see if he can help with this. All the best, Tom T >> Dear all, >> >> my run of phenix.mr_rosetta stops with: >> >> ******************* ERROR ENDING *************** >> Inconsistent query numbering >> >> ******************* ERROR ENDING *************** >> >> I attach script and logfiles. >> >> Any suggestions? >> >> Thanks >> >> Pietro >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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Phaser searching with density: how do I place my model on the solution?
by Pietro Roversi 31 Jul '11

31 Jul '11

Dear all, I succeded in finding a molecular replacement solution searching with the density I have in P43212 against a C2221 dataset, using the Phaser procedure documented in: http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model Question: what operators should I use for dmmulti now? Or put it another way, how do I put onto the C2221 placement my P43212 model? I tried using the Euler and xyz numbers fro0m the phaser sol file but they do not seem to produce a model that goes with the C2221 Phaser density. Any help is greatly appreciated Thanks Pietro

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getting phenix and coot to talk on OSX
by Harry Greenblatt 31 Jul '11

31 Jul '11

BS"D Dear All, I see that CCP4 has a new version of coot for OSX that runs under X-windows. I'm not interested in using Fink, and Bill Scott's standalone binaries don't seem to work on my laptop, and we also have some machines at 10.5.x, and new versions of coot in that format are not available. But the CCP4 version wasn't built it to communicate with Phenix during a run. Is that functionality something that can be added easily post-facto? Thanks Harry ------------------------------------------------------------------------- Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenblatt(a)weizmann.ac.il Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel

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Third issue of Computational Crystallography Newsletter
by Nigel Moriarty 28 Jul '11

28 Jul '11

Dear Colleagues, I am pleased to announce the publication of the third issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. Articles -------- Improved target weight optimization in phenix.refine Mite-y lysozyme crystal and structure Short communications -------------------- A lightweight, versatile framework for visualizing reciprocal-space data An extremely fast spotfinder for real-time beamline applications Hints for running phenix.mr_rosetta Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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C=O-D(+) and COOD restraints for phenix.refine
by Maxime Cuypers 28 Jul '11

28 Jul '11

Hello, Apologies if this problem has been asked previously, but i can t seem to find a solution online. I have added deuterium atoms in an exotic part of amide group (main chain) R2-C=O-D (+) bond and on a side chain Glu R-COOD to my pdb. i need to get a .cif that would account for it and work with phenix.refine. However, ready_set does not create a .cif file for it as it does not find unrestrained atoms. "No unknown residues" i have formatted the pdb the following way, adding DX for example (see ***): ATOM 778 N GLU A 51 8.057 40.510 -2.596 1.00 9.23 N ATOM 779 CA GLU A 51 8.846 41.709 -2.789 1.00 10.29 C ATOM 780 CB GLU A 51 8.151 42.937 -2.157 1.00 10.64 C ATOM 781 CG GLU A 51 6.672 43.097 -2.610 1.00 14.50 C ATOM 782 CD GLU A 51 6.543 43.007 -4.130 1.00 12.87 C ATOM 783 OE2 GLU A 51 6.056 42.014 -4.689 1.00 12.79 O ATOM 784 OE1 GLU A 51 6.987 43.967 -4.788 1.00 14.44 O ATOM 785 C GLU A 51 10.293 41.604 -2.286 1.00 8.42 C ATOM 786 O GLU A 51 10.961 42.627 -2.213 1.00 11.96 O ATOM 787 D GLU A 51 7.625 40.435 -1.776 1.00 10.15 D ATOM 788 DA GLU A 51 8.957 41.874 -3.812 1.00 12.62 D ATOM 789 DB2 GLU A 51 8.172 42.833 -1.173 1.00 11.93 D ATOM 790 DB3 GLU A 51 8.654 43.758 -2.380 1.00 13.79 D ATOM 791 DG2 GLU A 51 6.159 42.376 -2.149 1.00 11.66 D ATOM 792 DG3 GLU A 51 6.340 43.998 -2.326 1.00 14.27 D ***ATOM 793 DE1 GLU A 51 8.271 44.322 -5.268 1.00 30.00 D ATOM 850 N LEU A 56 20.084 37.831 -2.359 1.00 10.58 N ATOM 851 CA LEU A 56 21.370 38.483 -2.643 1.00 11.42 C ATOM 852 CB LEU A 56 21.801 39.360 -1.449 1.00 12.58 C ATOM 853 CG LEU A 56 20.783 40.461 -1.081 1.00 14.37 C ATOM 854 CD1 LEU A 56 21.278 41.264 0.152 1.00 16.71 C ATOM 855 CD2 LEU A 56 20.512 41.416 -2.257 1.00 17.46 C ATOM 856 C LEU A 56 22.415 37.441 -2.957 1.00 14.27 C ATOM 857 O LEU A 56 23.025 36.818 -2.093 1.00 30.34 O ATOM 858 D LEU A 56 19.954 37.597 -1.492 1.00 11.35 D ATOM 859 DA LEU A 56 21.249 39.065 -3.470 1.00 11.59 D ATOM 860 DB2 LEU A 56 21.898 38.760 -0.652 1.00 14.27 D ATOM 861 DB3 LEU A 56 22.681 39.834 -1.676 1.00 14.15 D ATOM 862 DG LEU A 56 19.925 39.988 -0.873 1.00 15.72 D ATOM 863 DD11 LEU A 56 20.622 41.969 0.365 1.00 17.87 D ATOM 864 DD12 LEU A 56 21.385 40.668 0.910 1.00 17.46 D ATOM 865 DD13 LEU A 56 22.131 41.691 -0.060 1.00 18.41 D ATOM 866 DD21 LEU A 56 19.968 42.175 -1.959 1.00 18.01 D ATOM 867 DD22 LEU A 56 21.384 41.721 -2.564 1.00 16.67 D ATOM 868 DD23 LEU A 56 20.043 40.956 -2.972 1.00 18.06 D ***ATOM 869 DX LEU A 56 22.482 36.144 -2.004 0.20 30.00 D I suspect i need to find a correct name for the D atoms, but i tried several already unsuccessfully. phenix.refine complains about 2 unrestrained atoms, the 2 D. Does someone know if there is a way to solve this issue or a workaround, please? thanks, Maxime

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running geometry regularization on side chains only
by Francois Berenger 28 Jul '11

28 Jul '11

Hello, Is it possible to do phenix.pdbtools model.pdb --geometry_regularization but only allow sidechains to be corrected during the process? Thanks a lot, Francois.

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Syntax Question
by Yuri 27 Jul '11

27 Jul '11

What is the syntax for refining occupancies of all the objects with ALTLOC assignments? thnkyou -- Yuri Pompeu

2 1

phenix.phaser params.eff output directory
by G Y 26 Jul '11

26 Jul '11

Dear all, I am writing a script for phenix.phaser. The keyword "output_dir" seems not work. In params.eff file I give it a line like: solution = None output_dir = /home/.../somedir/ keywords { general { root = "PHASER" title = "[no title set]" verbose = None debug = None mute = None xyzout = ON hklout = ON jobs = 2 } But I can not generate output file in the specified directory(somedir in the above case). The output files are always put in current working directory. Did I choose a wrong keyword to do this? What would be the correct way? Any answer would be appreciate greatly. Many thanks. regards, GP

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Wrong e-mail, sorry
by Yuri 26 Jul '11

26 Jul '11

Please disregard the cif message... -- Yuri Pompeu

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roche.cif
by Yuri 26 Jul '11

26 Jul '11

data_comp_list # loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level DRG DRG 'DRG ' non-polymer 16 8 . # # --------------- # data_comp_DRG # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge DRG CAB C CH3 0.094 DRG HAC H HCH3 0.014 DRG HAD H HCH3 0.013 DRG HAE H HCH3 0.013 DRG OAF O O2 -0.092 DRG CAH C C 0.233 DRG OAC O O -0.406 DRG CAG C C 0.004 DRG CAA C C2 0.033 DRG HAB H HC2 0.013 DRG HAA H HC2 0.013 DRG CAE C CH2 0.096 DRG HAF H HCH2 0.013 DRG HAG H HCH2 0.013 DRG OAD O OH1 -0.098 DRG HAH H HOH1 0.044 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type DRG CAB n/a OAF START DRG HAC CAB . . DRG HAD CAB . . DRG HAE CAB . . DRG OAF CAB CAH . DRG CAH OAF CAG . DRG OAC CAH . . DRG CAG CAH CAE . DRG CAA CAG HAA . DRG HAB CAA . . DRG HAA CAA . . DRG CAE CAG OAD . DRG HAF CAE . . DRG HAG CAE . . DRG OAD CAE HAH . DRG HAH OAD . END loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd DRG CAB HAC single 1.090 0.029 DRG CAB HAD single 1.090 0.029 DRG CAB HAE single 1.090 0.029 DRG OAF CAB single 1.430 0.025 DRG CAH OAF single 1.360 0.022 DRG CAH OAC double 1.230 0.017 DRG CAH CAG single 1.530 0.025 DRG CAG CAA double 1.530 0.025 DRG CAG CAE single 1.530 0.025 DRG CAA HAB single 1.090 0.029 DRG CAA HAA single 1.090 0.029 DRG CAE HAF single 1.090 0.029 DRG CAE HAG single 1.090 0.029 DRG CAE OAD single 1.430 0.025 DRG OAD HAH single 1.000 0.027 loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd DRG HAC CAB HAD 109.500 3.333 DRG HAC CAB HAE 109.500 3.333 DRG HAC CAB OAF 109.500 3.333 DRG HAD CAB HAE 109.500 3.333 DRG HAD CAB OAF 109.500 3.333 DRG HAE CAB OAF 109.500 3.333 DRG CAB OAF CAH 109.500 3.717 DRG OAF CAH OAC 124.000 2.502 DRG OAF CAH CAG 115.000 2.505 DRG OAC CAH CAG 121.000 2.494 DRG CAH CAG CAA 115.000 2.505 DRG CAH CAG CAE 115.000 2.505 DRG CAA CAG CAE 115.000 2.505 DRG CAG CAA HAB 115.000 2.505 DRG CAG CAA HAA 115.000 2.505 DRG HAB CAA HAA 120.000 2.989 DRG CAG CAE HAF 109.500 3.333 DRG CAG CAE HAG 109.500 3.333 DRG CAG CAE OAD 109.500 2.717 DRG HAF CAE HAG 109.500 3.333 DRG HAF CAE OAD 109.500 3.333 DRG HAG CAE OAD 109.500 3.333 DRG CAE OAD HAH 109.500 3.139 loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period DRG var_001 HAC CAB OAF CAH 60.000 4.440 3 DRG var_002 CAG CAH OAF CAB 60.000 4.440 3 DRG CONST_001 CAE CAG CAH OAF 180.000 0.714 2 DRG CONST_002 HAA CAA CAG CAH 180.000 0.714 2 DRG var_003 OAD CAE CAG CAH 30.000 16.736 6 DRG var_004 CAG CAE OAD HAH 60.000 13.289 3 loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign DRG chir_001 CAB HAC HAE HAD positiv DRG chir_002 CAE CAG HAG HAF positiv loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd DRG plan-01 OAF 0.030 DRG plan-01 CAH 0.030 DRG plan-01 OAC 0.030 DRG plan-01 CAG 0.030 DRG plan-01 CAA 0.030 DRG plan-01 HAB 0.030 DRG plan-01 HAA 0.030 DRG plan-01 CAE 0.030 # # --------------- # -- Yuri Pompeu

1 0

mr_rosetta with fixed solutions for other chains
by Bard, Joel 26 Jul '11

26 Jul '11

Hi- We have data for a crystal where two of three components have high homology search models and can be found with straightforward phaser runs but the third component has much weaker homology to anything in the pdb. Is there a way to provide the solution for the first two components and let mr_rosetta work on the third? Thanks, Joel

2 1

cif file for internal bond with one of two alternative conformations
by Daqi Tu 26 Jul '11

26 Jul '11

Hi, I have a structure of drug bound to a protein. The drug has two alternative conformations, in which one of them has an internal bond making it a cyclic compound. How do I refine a structure like this? What modification should I do to its cif file, which I generated using elbow without the internal bond. Thank you. Daqi Tu (sorry if I have double posted.)

2 1

phenix.phaser params.eff labin problem
by G P 25 Jul '11

25 Jul '11

Dear all, I am now writing a script for phenix.phaser. In the input file params.eff there is a keyword labin which corresponds to the labels inside input mtz files. The important columns in my ccp4 mtz file are FP, SIGFP. I edit the line of labin as: labin F=FP SIGF=SIGFP when running the script, it returns me: Syntax error: expected "=", found "F" (file "params.eff", line 9) So, I changed it like: labin=FP SIGFP when running, it gave me the message: Sorry: Couldn't find array FP SIGP in file I also tried: labin="FP" or labin = "FP SIGFP" or labin="labin F=FP" and so on. With nothing it can find the right columns. My mtz file should be not problem, I checked with mtzdmp, the columns FP and SIGFP were there and with phenix GUI this file works well. Would someone know exactly how to edit this line in params.eff? Many thanks! GP

3 7

Alternate conformer and HOH clashes
by Yuri 25 Jul '11

25 Jul '11

Thanks guys... What about waters, do they follow the same ALTLOC rules? I have a high res data 1A and I see lots of things... Ill probably bother you again with some questions as I keep refining. Best, Yuri -- Yuri Pompeu

2 1

Alternate conformer and HOH clashes
by Yuri 24 Jul '11

24 Jul '11

Dear All, I am having trouble refining multiple conformers that would clash into a neighbouring side chain that also has an alternate conformer. An attempt to clarify: Lets say a Tyr residue has conformation A1, but also moves into a position B1. In postition B, its side chain would clash into a neighbour Phe A2. However this Phe has another conformation B2. Bottom line, B1 and B2 would not clash, neither would A1 and A2. Any other combo (A1 B2, etc...) would clash. When I model it all in I see problems... I encounter the same situation with partially occupied HOHs. Whats the best way to deal with this Thank you -- Yuri Pompeu

3 2

Latest Build Error
by Yuri 22 Jul '11

22 Jul '11

I installed the latest dev-826 version and the GUI does not open phenix_refine. I get a fatal error message. thank you -- Yuri Pompeu

2 1

restraints for D3O+ give problems to run in phenix.refine
by Maxime Cuypers 22 Jul '11

22 Jul '11

hello, apologies if this problem has already been reported, i browsed for a while and i am running out of ideas to solve my problem. i have a neutron structure i was refining fine with phenix.refine untill i had to add a D3O water. description: running phenix.elbow or phenix.refine with .cif file for D3O i am getting the following error: ... Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O D3O W 1 " occ=0.53 ... (2 atoms not shown) pdb=" D3 D3O W 1 " occ=0.53 Number of atoms with unknown nonbonded energy type symbols: 3 "HETATM 2 D1 D3O W 1 .*. D " "HETATM 3 D2 D3O W 1 .*. D " "HETATM 4 D3 D3O W 1 .*. D " Time building chain proxies: 0.01, per 1000 atoms: 2.50 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 3 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). ******************* i then modified the .param file implementing the apply_cif_modification and apply_cif_link parameters: refinement { main { number_of_macro_cycles = 10 ordered_solvent= false scattering_table= neutron } hydrogens { refine= individual } pdb_interpretation.apply_cif_modification { data_mod = D3O residue_selection = resname D3O } pdb_interpretation.apply_cif_link { data_link = D3O residue_selection_1 = chain W and resname D3O } } ... ************************** the .cif file i have was created with phenix.ready_set: ( i added first line after it failed without) data_mod_D3O # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level D3O D3O Unknown ligand 4 1 . # data_comp_D3O # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z D3O O O O -0.475 -12.5180 -14.4044 -43.0985 D3O H1 D D -0.294 -11.4013 -13.8002 -42.6392 D3O H2 D D -0.294 -13.3333 -13.3284 -43.0933 D3O H3 D D 0.063 -12.3324 -14.5311 -44.0190 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd D3O O H1 single 1.350 0.040 D3O O H2 single 1.350 0.040 D3O O H3 single 0.947 0.010 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd D3O H2 O H1 98.14 3.000 D3O H3 O H1 103.20 1.194 D3O H3 O H2 103.22 1.252 ********************************** whatever i do i systematically get the same error: Monomer Library directory: "/usr/local/phenix-1.7.1-743/chem_data/mon_lib" Total number of atoms: 1165 Number of models: 1 apply_cif_modification: data_mod: D3O Sorry: Missing CIF modification: data_mod_D3O Please check for spelling errors or specify the file name with the modification as an additional argument. ******************************** the command i enter is: phenix.refine xxxx.pdb xxxx.mtz D3O.ligands.cif high_res_xxxx-neutron-long-D3O.params \ refinement.input.xray_data.labels='IMEAN,SIGIMEAN' i looked in the online phenix.refine manual but it is not mentionning what to do in such error case. where should i put "data_mod_D3O" in the parameter file? is it the real source of the error? Could someone help me figuring out a solution to get the restraints to work for D3O(+), please? Maxime

3 2

Protein expression, purification and crystallization
by Hena Dutta 21 Jul '11

21 Jul '11

Dear Members of CCP4BB and PHENIXBB, Can you suggest a reliable website where I can get basic and advanced information on protein expression, purification and crystallization. I like to read on the monitor. Thanking you in advance... Hena

2 1

phenix.phaser PATH problem
by G P 21 Jul '11

21 Jul '11

Dear all, It's long story: At beginning, I have phenix installed. I do not have CCP4 installed. Then I run "phenix.phaser params.eff" to call phenix run phaser from script params.eff. It works well. Then, I installed CCP4 with its own phaser inside. Then I run again "phenix.phaser params.eff". The computer start to import files (should be some libraries and supporting files, not input data) from CCP4 installation directory. It seems so strange for me. And because some of the .so files in CCP4 directory are for 32bit, phenix.phaser gave me error message: wrong ELF class: ELFCLASS32 and refused to keep running. I guess I could solve this problem by copying the same .so file in phenix directory into CCP4's directory. What I really want to know is why this happen. Is that the installation of CCP4 changed some kinds of PATH variables for phenix? How could I fix by giving a right path again? I would appreciate to any help. Thanks a lot guys! Best regards, GP

4 6

phenix.phaser multiple models
by G Y 21 Jul '11

21 Jul '11

Dear all, I want to give several input pdb (searching model) at same time and let phaser run MR separately on each of them. I found I can do this by first "Add ensembles" at Ensemble tab and then "Add search" at Search procedure tab then link the correct ensemble ID. However, there is just one output result for the best solution. Is there anyway to get all solutions in separate .mtz and .pdb files for different searching models? Many thanks! regards, G

2 1

problem in rosetta rebuilding
by intekhab alam 21 Jul '11

21 Jul '11

Hi i tried to run rosetta on a unix machine (ubuntu 9.04) for my data. Upto MR step everything goes fine , but during the rebuilding step after 20 cycles the computer shuts down. i have attached the log file for the autobuilding run of rosetta. i am using phenix 1.7.1-743 version. i will be grateful if some one helps me out -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

3 3

Phenix TLS refined model feeding into next round of refinement
by Daqi Tu 20 Jul '11

20 Jul '11

Hi, I used to think after one round of Phenix TLS refinement, if I need to do further refinements after correcting couple residues, I need to take out the ANISOU records from the pdb file. The reason is if not, all protein atoms might be applied anisotropic individual B factor refinement in the next round. Yesterday, I made a "mistake" directly feeding the pdb file from the previous TLS refinement into the next one. Seems it is fine. Is that true Phenix automatically recognize what I wanted, that is, TLS only, not anisotropic individual B factor refinement? Thank you. Daqi Tu

2 2

How the sharpening were performed in PHENIX.
by zhangh1＠umbc.edu 20 Jul '11

20 Jul '11

Hi, I was trying to do a B-factor sharpening using phenix GUI CreatMaps utilities. The output for the sharpened maps contains 2FOFCWT and PHI2FOFCWT columes, so I think they are sigmaA weighted 2Fo-Fc maps. But from Brunger's paper, the sharpening coefficients seems directly applied on Fo, and I wonder what happened before we get the 2mFoDFc maps. Or, the sharpening coefficients have been applied to the 2mFoDFc maps? Thanks for any information! Hailiang

2 2

Experimental Data Question
by Yuri 16 Jul '11

16 Jul '11

Nat, That helps clarifying things. Thank you -- Yuri Pompeu

1 0

Experimental Data Question
by Yuri 16 Jul '11

16 Jul '11

It looks like phase_and_build only takes reflections input as F SIGF. I had to use a reflection converter as I had a .sca file with I SIGI data. -- Yuri Pompeu

2 1

Re: [phenixbb] Experimental Data Question
by Yuri 15 Jul '11

15 Jul '11

I am not positive, because I had to convert my reflections.sca (I SIGI) into reflections.mtz (F SIGF) -- Yuri Pompeu

2 1

Experimental Data Question
by Yuri 15 Jul '11

15 Jul '11

Hello All, Heres my situation: I collected data on a new crystal, indexed, scaled (2.75 A), ran molecular replacement (40% homologue) and found a solution. I did some building got a new model, did an initial refinement (using my .sca file, not data.mtz from mol rep). I then ran phase_and_build with density modification. The new maps look a lot better and I am able to see some residues I was not able to place before. I did some more building and I am ready to refine. What should I use as experimental data? phase and_build gave me a .mtz file with amplitudes (no I) and "experimental phase" coeeficients (HLAM. HLBM,...) Cheers -- Yuri Pompeu

2 1

Re: [phenixbb] ADP refinement selection
by Pavel Afonine 15 Jul '11

15 Jul '11

Hi Christian, the problem is that you did not ask phenix.refine to refine the rest of the atoms isotropically (with your command below you only refine anisotropic ADPs of atoms in chain Q, and the B-factors of all the other atoms are not refined): > adp { > individual { > anisotropic = "chain Q" > } I would do it like this: adp { individual { anisotropic = chain Q and element CL isotropic = not (chain Q and element CL) } } Pavel.

2 2

off-topic-Question
by Haytham Wahba 14 Jul '11

14 Jul '11

Dear all i have protein soaked in Dimethyltindibromide in the active site 2 cysteine and 1 aspartic acid by help of anomalous map i can see 2 Sn atoms in each subunit in AU there is difference in both subunits, Sub-A shows acetate near Sn and Sub-B show phosphate ion, even the position of one of the 2 cystein is different from unit to other 1-is it normal to see such difference between 2 subunit? also the distances between Sn and surrounding atoms does not suggest covalent binding 2-the important question is how to confirm if the 2 methyl groups or even one methyl group of dimethlytin are still there or cleaved i mean one can not differentiate between density of water and methygroup. How to define coordinate number of Heavy atom and identity of the attached atoms as you will see in the link below (with water) and (with Methyl) the map are the same and as well r-factors 3-what can i do to confirm presence or cleavage of methyl: collect more data or using other technique like exafs, Mossbauer spectroscopy could help (with water) http://dl.dropbox.com/u/12001878/Subunit-A.png http://dl.dropbox.com/u/12001878/subunit-A-anomalous.png http://dl.dropbox.com/u/12001878/Subunit-B.png http://dl.dropbox.com/u/12001878/subunit-B-anomalous.png (with methyl) http://dl.dropbox.com/u/12001878/DimethylTin-subunit-A-alt-conf.png http://dl.dropbox.com/u/12001878/DimethylTin-subunit-B.png N.B: resolution 1.7 A r factors and molprop are perfect. thank you for your time haytham biochimi canada

1 0

Parsing error
by Yuri 14 Jul '11

14 Jul '11

Nat, Thank you. I am still using dev-814. You probably have fixed it already. ill update when I am done running these jobs. -- Yuri Pompeu

1 0

Parsing error
by Yuri 14 Jul '11

14 Jul '11

Hello everyone, I cannot figure out why I keep getting this error. I dont see anything wrong with my PDB. I realize I realize I have breaks in my chain, as there are regions of unclear density as of now I am building in what I can see... Heres what the log says: ======== ================= Separating polymer chains into rigid bodies ================= (chain 'A' and segid ' ' and resseq 393:6) (chain 'B' and segid 'B ' and resseq 401:401) ================== Extract refinement strategy and selections ================= The error is initial RESSEQ index > final RESSEQ index. I do not understand why it is picking them this way It then halts at an error... Any Ideas?

3 4

restraints_edite.params
by Haytham Wahba 13 Jul '11

13 Jul '11

Dear All How to get rid of restraints_edite.params in the following run of phenix.refine, i mean after using it in previous run.and what is .def files. and bond.slack Haytham Udem Biochemi Canada

4 3

R-merge and MOLREP
by Yuri 13 Jul '11

13 Jul '11

Ed and Nathaniel, Thank you for the input. I agree with Ed. The I/sigma values for this data set are well within accepted ranges... I believe the R-merge values are due to some inherent crystal property. They grew in very strange manner. -- Yuri Pompeu

1 0

R-merge and MOLREP
by Yuri 13 Jul '11

13 Jul '11

Hello everyone, I just collected some data on a new protein. It indexes in P3 and looks like I can scale it all the way to P 63 2 2 . My questions are: 1-I see a reasonable chi-square value 1.69 but r-merge 0.15 (0.49 at 2.75 A). It was 0.20 before I excluded some bad frames. I thought this R value is a bit high... Is it? Mosaicty was around 1.00. 2- My search model has an identity of around 40%. I tried MOLREP. Seems I got a solution LLG=486 PAK=10 TFZ ~30 RFZ ~20. My R-free before any refinement is 0.54. Two questions here, a) I think I only fully understand the meaning of LLG, what about PAK and both Z-values? b)is this R-free acceptable or is it also a little high? Thank you for any input

3 2

Summer X-rays at the NSLS
by Robert Sweet 11 Jul '11

11 Jul '11

Summer X-rays at the NSLS The PXRR operates five beamlines at the NSLS: http://www.px.nsls.bnl.gov/. Two of these are the undulator beamlines X25 and X29. The dipole beamlines X12-B and X12-C are available, and are very effective for conventional crystallography. There are efficient ALS-Style Automounters available -- 8400 crystals mounted in the last 12 months. Also, at beamline X26-C, we have a unique-in-the-US station for combined x-ray diffraction and single-crystal optical spectroscopies: http://www.px.nsls.bnl.gov/x26c/x26c_info.html Notice also our world-leading Mail-In crystallography program: http://www.px.nsls.bnl.gov/Mailin.html You may request access to any of these here: http://www.px.nsls.bnl.gov/beamtime_requests.html, and can look at the schedules for all five here: http://www.px.nsls.bnl.gov/ Stay tuned for the announcement in December of RapiData, our annual course in rapid data collection and structure solving: http://www.bnl.gov/rapidata/ Bob Sweet ========================================================================= 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/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

11 19

significant figures in reporting Rfree
by Jennifer Weinreich 11 Jul '11

11 Jul '11

Hi. I am wondering what is the common practice with respect to how many significant figures should be used for reporting Rfree at different resolution? Should we always use all 4 figures that are reported by the program? Thank you, Jenn

4 4

How to rebuild a molecular only‏
by dingding830106＠sina.com 09 Jul '11

09 Jul '11

Dear All, There are 8 moleculars in an asymmetry unit, but only one molecular should be rebulit, what can I do ? Thanks a lot! Wei Feng

2 1

Re: [phenixbb] Elbow and smiles to make CO coordinates
by Yarrow Madrona 08 Jul '11

08 Jul '11

Thanks! Didn't realize it was so easy. > For getting carbon monoxide coordinates: In coot, go to File > Get > Monomer... > Type in "CMO" and click OK. > > A carbon monoxide molecule will po up in the middle of the window > (provided everything is set up correctly). > > If you are trying to fit an electron density, place that density in the > middle of the window before you retrieve the ligand. > > Hope that helps. > > Cheers! > MM > > On Jul 8, 2011, at 1:41 PM, Yarrow Madrona wrote: > >> >> Hi, >> >> I am trying to use Elbow and smiles to generate carbon monoxide >> coordinates. I thought it would be easy enough. I made two waters in >> coot >> and changed the the oxygens to C and O and set the distance around 1.13 >> angstrom. Saved these coordinates as a PDB. I then used this in Elbow >> but >> it gives me a methyl group. Not sure what is going on. Any help would >> be >> appreciated. Thank you! >> >> -Yarrow >> >> -- >> Yarrow Madrona >> >> Graduate Student >> Molecular Biology and Biochemistry Dept. >> University of California, Irvine >> Natural Sciences I, Rm 2403 >> Irvine, CA 92697 >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

1 0

Elbow and smiles to make CO coordinates
by Yarrow Madrona 08 Jul '11

08 Jul '11

Hi, I am trying to use Elbow and smiles to generate carbon monoxide coordinates. I thought it would be easy enough. I made two waters in coot and changed the the oxygens to C and O and set the distance around 1.13 angstrom. Saved these coordinates as a PDB. I then used this in Elbow but it gives me a methyl group. Not sure what is going on. Any help would be appreciated. Thank you! -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

3 2

AutoSol question
by Laurie Betts 08 Jul '11

08 Jul '11

If I want to run Autosol with a set of previously determined heavy atom positions (seleno-Met protein) that I might have edited, and NOT search for any more sites, just use those sites for phasing and density modification and model building, I can't seem to find in any of the parameter buttons a way to do this - every time I try it seems to just re-run hyss and find the same sites again. It seems to find multiple Se sites on top of each other that are closer than the minimum distance I specified in the input. Thanks LAurie Betts

2 1

NCS Question
by Yuri 07 Jul '11

07 Jul '11

Dear PHENIX community, Could someone please point me toward a good paper on NCS? Cheers, -- Yuri Pompeu

3 2

SA omit map
by Tjaard Pijning 06 Jul '11

06 Jul '11

Hi, I would like to generate an SA-omit Fo-Fc map for a ligand bound to protein. Using the GUI I selected the AutoBuild-Create Omit Map module and set the following : - data.mtz - protein.pdb (no ligand, no solvent) = start model - ligand.pdb (just ligand) = omit map atoms - omit map type = simulated annealing - omit region = omit around pdb The resulting map (/OMIT/resolve_composite_map.mtz) shows density for both the protein and the ligand. When I feed this into the CCP4 module FFT to generate an nF1-mF2 map (with n=1 and m=1) I still get density for both the protein and ligand. However I need only the ligand Fo-Fc density. What is the right way to do this ? Thanks, Tjaard Ing. Tjaard Pijning Research Assistant Protein Crystallography Group Nijenborgh 7 9747 AG Groningen The Netherlands (31)(0)50 363 43 85

4 6

Re: [phenixbb] phenix.mr_rosetta: Inconsistent query numbering
by Thomas C. Terwilliger 06 Jul '11

06 Jul '11

Hi Pietro, There is something that phenix.mr_model_preparation cannot read in Japanin.hhr (attached): phenix.mr_model_preparation Japanin.hhr gives the same error. I'll copy Gabor Bunkoczi and see if he can help with this. All the best, Tom T >> Dear all, >> >> my run of phenix.mr_rosetta stops with: >> >> ******************* ERROR ENDING *************** >> Inconsistent query numbering >> >> ******************* ERROR ENDING *************** >> >> I attach script and logfiles. >> >> Any suggestions? >> >> Thanks >> >> Pietro >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

3 2

Validation question: R-factor (all) and # of unique reflections (all)
by Young-Jin Cho 05 Jul '11

05 Jul '11

Hi everyone, While I am trying to deposit, I am faced with several things that I am not sure: FYI. I am in the <Refinement Statistics> section (Auto Dep Input Tool) in the PDB bank. Most values are came from pdb file that was made from phenix.refine but it asks me "R-factor (all)" that satisfy the limits established by high & low resolution cut off and "number of unique reflections (all)". My simple question is if phenix has those kind of information, if so where I can find them. Another question is if I changed water (deletion or changed occupancy) based on 'precheck', should I run phenix.refine again to get R/Rfree values in correct? I am not sure if these are captured by PDB automatically or not. (seemingly they do like that at this point but not 100% sure yet.) With many thanks~ Young-Jin

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Re: [phenixbb] Validation question: R-factor (all) and # of unique reflections (all)
by Pavel Afonine 05 Jul '11

05 Jul '11

Hi Young-Jin, > I feel like I should calculate R(all). As mtz file is usually big, > how can I extract Fobs and Fmodel from phenix generated mtz file? If you feel you want it, then go ahead, and this command might be of help here: phenix.mtz.dump data.mtz --column-data-format=spreadsheet -c Yet another (easier) alternative is to run a dummy phenix.refine run like this: phenix.refine data.mtz model.pdb xray_data.r_free_flags.ignore_r_free_flags=true main.number_of_mac=1 strategy=none output.prefix=junk then take the reported R-factor (Rwork will be equal to Rfree, so take any of them), and discard the files. All the best! Pavel.

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phenix.mr_rosetta: Inconsistent query numbering
by Pietro Roversi 05 Jul '11

05 Jul '11

Dear all, my run of phenix.mr_rosetta stops with: ******************* ERROR ENDING *************** Inconsistent query numbering ******************* ERROR ENDING *************** I attach script and logfiles. Any suggestions? Thanks Pietro

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Ligand woes
by José Trincão 05 Jul '11

05 Jul '11

Hello all, I have been having very weird problems refining a structure with several ligands. The weirdest problem is that if I try to run ligand fit giving just the name of the ligands, no problem - it finds the ligands (FAD and MTE). I save the pdb with all the ligands in and phenix.refine complains that MTE is not recognised, I have to run ready-set. I do it. Run phenix.refine again, and now it complains with the following: Number of atoms with unknown nonbonded energy type symbols: 116 "HETATM18439 C1' MTE A3003 .*. C " "HETATM18441 C2' MTE A3003 .*. C " "HETATM18443 C3' MTE A3003 .*. C " "HETATM18444 O3' MTE A3003 .*. O " "HETATM18474 N9A FAD A3005 .*. N " "HETATM18475 C8A FAD A3005 .*. C " "HETATM18476 N7A FAD A3005 .*. N " "HETATM18477 C5A FAD A3005 .*. C " "HETATM18478 C6A FAD A3005 .*. C " "HETATM18480 N1A FAD A3005 .*. N " ... (remaining 106 not shown) Any help will be greatly appreciated. Jose José Trincão, PhD CQFB@FCT-UNL 2829-516 Caparica, Portugal "It's very hard to make predictions... especially about the future" - Niels Bohr

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NCS Restraints
by Yuri 01 Jul '11

01 Jul '11

Hi Pavel, >It's rather packing.. Say, if more than one copy packs in the > asymmetric >unit then you have NCS, roughly speaking.. So is it correct to say that in cases where you have 1 molecule per ASU, there will be no NCS only crystallographic symmetry?? > In other words, if for the same enzyme one crystal goes to 3.1 and > another 1.5 A could one have significant NCS but not the other? >I'm not sure I understood this... May some one else did? I was trying to understand if this phenomenon would be noticeable depending on the resolution only... You and Nathaniel pretty much answered this now... -- Yuri Pompeu

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NCS restraints
by Yuri 01 Jul '11

01 Jul '11

Hello, I have some fundamental questions about NCS: 1- I think its somewhat of a consensus that at higher res. it should not be used to avoid missing out "real" detailed discrepancy. Is this true? 2- Should one try to use it in lower res data (3 A and worse)? 3- Is the presence of NCS macromolecule specific, or crystal specific? In other words, if for the same enzyme one crystal goes to 3.1 and another 1.5 A could one have significant NCS but not the other? Thanks or any clarification -- Yuri Pompeu

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