- phenixbb - phenix-online.org

Intensity-Weighted Reciprocal Lattice
by Michael Thompson 05 Aug '11

05 Aug '11

Hello ccp4 & phenix BB members, I would like to view the intensity-weighted reciprocal lattice for several data sets that I have collected. (The data have been indexed, integrated and scaled with Denzo and Scalepack.) I was wondering if anyone could offer some advice on what might be the best and/or most practical way to do this? I know that there are several programs out there that can generate sections (i.e. 0,k,l) of the reciprocal lattice, such as LABELIT and xrayplot. Are there any other options for doing this, perhaps within ccp4 and/or phenix? I once saw someone give a presentation and they had a little video that showed a three dimensional section of the reciprocal lattice rocking back and forth, which was really cool. I liked this because I felt like it gave a much more holistic representation as opposed to viewing a bunch of individual sections. I don't know if there is an easy way to do this, or if this person somehow managed to create this 3D depiction from a series of sections. Any tips or recommendations would be appreciated. Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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adding hydrogens -> increasing clash score
by Tatyana Sysoeva 05 Aug '11

05 Aug '11

Hi! I have probably a very naive question - when one includes hydrogens into a refinement of a model build with data at ~3.6A clash score should not go up? I mean I am including hydrogens for a reason of improving the model quality when I cannot fit the sidechains into some density, etc. Can it be true that using default 3 macrocycles on a changed (reduced) model is not enough to minimize it? Thanks, Tanya

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Alternate occupancies
by Yuri 04 Aug '11

04 Aug '11

Dear all, If tell phenix.refine to do occupancy refinement on resname HOH, will it still perform the default refinement for residues with alternate conformers? -- Yuri Pompeu

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how to apply phi/psi helical restraints
by Daqi Tu 03 Aug '11

03 Aug '11

Hi, I was trying to restrain a relatively mobile region of my structure to be helical using Phenix secondary structure restraints. The result is very bad. It forces the N-O distance to be about 3A, but the phi/psi angles are all ugly. What is the way in Phenix I can apply phi/psi restraints just like in the old CNS, which had always worked nicely? Thank you. Daqi Tu

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phenix.mr_rosetta
by Andreas Förster 02 Aug '11

02 Aug '11

Dear all, I've made the frightening plunge into the cold waters of Rosetta (3.3 this time) again, with an eye on using it with Phenix, and am sharing the joy. Things work, but: - Download rosetta_source and rosetta_database separately. The bundle doesn't contain all the files. - Compilation fails on RHEL 6.1 (gcc 4.5 issue) but sails on RHEL 5.5. - $PHENIX_ROSETTA_PATH must point to the Rosetta installation directory (where rosetta_source and rosetta_database sit). Don't be misled by the phenix.mr_rosetta documentation into setting $PHENIX_ROSETTTA_PATH (triple T). - all directories in the Rosetta installation must be made accessible to users find $PHENIX_ROSETTA_PATH -type d -exec chmod 755 '{}' \; Hope that helps someone. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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new optimize weight
by daqi tu 01 Aug '11

01 Aug '11

Hi, With Phenix dev-836, when optimize_xyz_weight and optimize_adp_weight are set to true, where can I find the optimal weights so I can directly put into the next run to save time (i.e. without optimizing any more). Previously it is a scale factor I can use for fix_wxc for example. But right now I can only see a weight factor. Thanks. Daqi

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Re: [phenixbb] Third issue of Computation Crystallography Newsletter - Volume 2, Number 2
by Frank von Delft 01 Aug '11

01 Aug '11

Hi, just scanned through the article on automatic weight adjustment. If I had to summarise figures 1 and 2, I'd have to conclude that the latest weight optimization only occasionally produces better results than not doing it (fig 2); and that therefore the old optimization was considerably worse than doing nothing at all. Or have I misinterpreted it? Cheers phx On 28/07/2011 19:59, Nigel Moriarty wrote: > 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 >

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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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