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Re: [phenixbb] problem in rosetta rebuilding
by intekhab alam 31 Jul '11

31 Jul '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 30 Jul '11

30 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 27 Jul '11

27 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 26 Jul '11

26 Jul '11

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

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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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