Posts by Mike

21) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69479) Posted 24 Jan 2011 by Mike Post: okay now here is an image of what it looks like when I am viewing my outputted structure prediction http://img199.imageshack.us/i/33216778.png/ Do you see the problem now?
22) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69472) Posted 22 Jan 2011 by Mike Post: okay now here is an image of what it looks like when I am viewing my outputted structure prediction http://img199.imageshack.us/i/33216778.png/
23) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69468) Posted 22 Jan 2011 by Mike Post: extract_pdbs. exe -in:file:silent default.out -database minirosetta_database core.init: Mini-Rosetta version 34709M from https://svn.rosettacommons.org/sourc e/trunk/mini core.init: command: extract_pdbs.exe -in:file:silent default.out -database minir osetta_database core.init: 'RNG device' seed mode, using 'CryptGenRandom', seed=96414181 seed_of fset=0 real_seed=96414181 core.init.random: RandomGenerator:init: Normal mode, seed=96414181 RG_type=mt199 37 Warning: Unable to locate database file chemical/atom_type_sets/fa_standard/ ERROR: ERROR: Unable to open silent_input file: 'default.out' ERROR:: Exit from: ....srccoreiosilentSilentFileData.cc line: 86 You need to run it in the same directory where default.out and minirosetta_database exists. It's not finding these. I'm not sure what's happening with your other post. May be an incompatible silent mode format which you will not be able to extract. I need the work unit names to look into these issues further. Not all results will be able to be extracted. Please keep this in mind. mem_widd_run03_centroid 2rlf and 2k73 PBID's
24) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69467) Posted 21 Jan 2011 by Mike Post: extract_pdbs. exe -in:file:silent default.out -database minirosetta_database core.init: Mini-Rosetta version 34709M from https://svn.rosettacommons.org/sourc e/trunk/mini core.init: command: extract_pdbs.exe -in:file:silent default.out -database minir osetta_database core.init: 'RNG device' seed mode, using 'CryptGenRandom', seed=96414181 seed_of fset=0 real_seed=96414181 core.init.random: RandomGenerator:init: Normal mode, seed=96414181 RG_type=mt199 37 Warning: Unable to locate database file chemical/atom_type_sets/fa_standard/ ERROR: ERROR: Unable to open silent_input file: 'default.out' ERROR:: Exit from: ....srccoreiosilentSilentFileData.cc line: 86 You need to run it in the same directory where default.out and minirosetta_database exists. It's not finding these. I'm not sure what's happening with your other post. May be an incompatible silent mode format which you will not be able to extract. I need the work unit names to look into these issues further. Not all results will be able to be extracted. Please keep this in mind. You can see the problem much better if you view the structure in a molecular viewing program as wireframe
25) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69463) Posted 21 Jan 2011 by Mike Post: extract_pdbs. exe -in:file:silent default.out -database minirosetta_database core.init: Mini-Rosetta version 34709M from https://svn.rosettacommons.org/sourc e/trunk/mini core.init: command: extract_pdbs.exe -in:file:silent default.out -database minir osetta_database core.init: 'RNG device' seed mode, using 'CryptGenRandom', seed=96414181 seed_of fset=0 real_seed=96414181 core.init.random: RandomGenerator:init: Normal mode, seed=96414181 RG_type=mt199 37 Warning: Unable to locate database file chemical/atom_type_sets/fa_standard/ ERROR: ERROR: Unable to open silent_input file: 'default.out' ERROR:: Exit from: ....srccoreiosilentSilentFileData.cc line: 86
26) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69462) Posted 21 Jan 2011 by Mike Post: .extract_pdbs.exe -in:file:silent default.out -database minirosetta_database -in::file::silent_struct_type 'protein' isn't working I need more info. What's being printed out to the terminal? Which work unit is it? e/trunk/mini core.init: command: extract_pdbs.exe -in:file:silent chk_S_00013_FragmentSampler __rg_state.out -database minirosetta_database core.init: 'RNG device' seed mode, using 'CryptGenRandom', seed=-1820135110 seed _offset=0 real_seed=-1820135110 core.init.random: RandomGenerator:init: Normal mode, seed=-1820135110 RG_type=mt 19937 Warning: Unable to locate database file chemical/atom_type_sets/fa_standard/ core.io.silent: Reading all structures from chk_S_00013_FragmentSampler__rg_stat e.out core.io.silent: Finished reading 1 structures from chk_S_00013_FragmentSampler__ rg_state.out core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy w ell core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. core.io.database: Database file opened: minirosetta_databasepdb_pair_stats_fine core.io.database: Database file opened: minirosetta_databasescoring/score_funct ions/hbonds/standard_params/HBPoly1D.csv core.io.database: Database file opened: minirosetta_databasescoring/score_funct ions/hbonds/standard_params/HBFadeIntervals.csv core.io.database: Database file opened: minirosetta_databasescoring/score_funct ions/hbonds/standard_params/HBEval.csv core.io.database: Database file opened: minirosetta_databaseP_AA.gz core.io.database: Database file opened: minirosetta_databaseP_AA_n.gz core.io.database: Database file opened: minirosetta_databaseP_AA_pp.gz core.io.database: Database file opened: minirosetta_databaseRama_smooth_dyn.dat _ss_6.4.gz core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 1 natoms_pose=14atm_seqpos 1 natoms _struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 2 natoms_pose=11atm_seqpos 2 natoms _struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 3 natoms_pose=22atm_seqpos 3 natoms _struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 4 natoms_pose=19atm_seqpos 4 natoms _struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 5 natoms_pose=11atm_seqpos 5 natoms _struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 6 natoms_pose=21atm_seqpos 6 natoms _struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 7 natoms_pose=19atm_seqpos 7 natoms _struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 8 natoms_pose=19atm_seqpos 8 natoms _struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 9 natoms_pose=12atm_seqpos 9 natoms _struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 10 natoms_pose=7atm_seqpos 10 natom s_struct=6) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 11 natoms_pose=19atm_seqpos 11 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 12 natoms_pose=19atm_seqpos 12 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 13 natoms_pose=20atm_seqpos 13 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 14 natoms_pose=19atm_seqpos 14 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 15 natoms_pose=21atm_seqpos 15 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 16 natoms_pose=7atm_seqpos 16 natom s_struct=6) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 17 natoms_pose=16atm_seqpos 17 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 18 natoms_pose=19atm_seqpos 18 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 19 natoms_pose=19atm_seqpos 19 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 20 natoms_pose=14atm_seqpos 20 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 21 natoms_pose=10atm_seqpos 21 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 22 natoms_pose=19atm_seqpos 22 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 23 natoms_pose=20atm_seqpos 23 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 24 natoms_pose=19atm_seqpos 24 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 25 natoms_pose=24atm_seqpos 25 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 26 natoms_pose=16atm_seqpos 26 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 27 natoms_pose=22atm_seqpos 27 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 28 natoms_pose=20atm_seqpos 28 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 29 natoms_pose=11atm_seqpos 29 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 30 natoms_pose=24atm_seqpos 30 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 31 natoms_pose=11atm_seqpos 31 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 32 natoms_pose=10atm_seqpos 32 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 33 natoms_pose=13atm_seqpos 33 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 34 natoms_pose=14atm_seqpos 1 natom s_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 35 natoms_pose=11atm_seqpos 2 natom s_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 36 natoms_pose=22atm_seqpos 3 natom s_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 37 natoms_pose=19atm_seqpos 4 natom s_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 38 natoms_pose=11atm_seqpos 5 natom s_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 39 natoms_pose=21atm_seqpos 6 natom s_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 40 natoms_pose=19atm_seqpos 7 natom s_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 41 natoms_pose=19atm_seqpos 8 natom s_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 42 natoms_pose=12atm_seqpos 9 natom s_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 43 natoms_pose=7atm_seqpos 10 natom s_struct=6) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 44 natoms_pose=19atm_seqpos 11 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 45 natoms_pose=19atm_seqpos 12 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 46 natoms_pose=20atm_seqpos 13 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 47 natoms_pose=19atm_seqpos 14 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 48 natoms_pose=21atm_seqpos 15 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 49 natoms_pose=7atm_seqpos 16 natom s_struct=6) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 50 natoms_pose=16atm_seqpos 17 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 51 natoms_pose=19atm_seqpos 18 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 52 natoms_pose=19atm_seqpos 19 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 53 natoms_pose=14atm_seqpos 20 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 54 natoms_pose=10atm_seqpos 21 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 55 natoms_pose=19atm_seqpos 22 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 56 natoms_pose=20atm_seqpos 23 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 57 natoms_pose=19atm_seqpos 24 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 58 natoms_pose=24atm_seqpos 25 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 59 natoms_pose=16atm_seqpos 26 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 60 natoms_pose=22atm_seqpos 27 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 61 natoms_pose=20atm_seqpos 28 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 62 natoms_pose=11atm_seqpos 29 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 63 natoms_pose=24atm_seqpos 30 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 64 natoms_pose=11atm_seqpos 31 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 65 natoms_pose=10atm_seqpos 32 nato ms_struct=7) core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! At tempting to continue ... core.io.silent: [ WARNING ] (in residue 66 natoms_pose=13atm_seqpos 33 nato ms_struct=7)
27) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69449) Posted 21 Jan 2011 by Mike Post: The first thing is I am getting a pdb file using your normal script that is all right except for an inexplicable entity in the center of it (I call it protein garbage, you may call it as you wish :) ) The second thing is the command line I posted many hours ago which technically should extract results from pdb silent file structs rather than binaries. But it is not working. The next time I have a rosetta work unit.... Probably tomorrow.... I will post the command line output.... but it should probably not be necessary because the protein garbage will probably happen on any computer running windows that runs the conversion program
28) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69445) Posted 20 Jan 2011 by Mike Post: .extract_pdbs.exe -in:file:silent default.out -database minirosetta_database -in::file::silent_struct_type 'protein' isn't working
29) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69427) Posted 19 Jan 2011 by Mike Post: I wasn't able to get the windows build to work. It will take some more time. You'll have to wait a few days because I have jury duty starting tomorrow. Sorry, but it's not trivial and requires a bit of work. If you have access to a mac or linux platform, you can get the extract_pdbs binaries at: http://boinc.bakerlab.org/rosetta/rah_misc/extractor/ you can run with -help to get command line options. basically you'll have to run a command like: extract_pdbs.macosgccrelease -in:file:silent default.out -database minirosetta_database in the slot directory that contains your result file and minirosetta_database. I'll post detailed instructions once I have the windows platform up. Yeh thanks David
30) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69421) Posted 19 Jan 2011 by Mike Post: did you try extracting with the old rosetta++ binary? depending on your platform: http://boinc.bakerlab.org/rosetta/download/rosetta_5.82_i686-apple-darwin http://boinc.bakerlab.org/rosetta/download/rosetta_5.82_i686-pc-linux-gnu http://boinc.bakerlab.org/rosetta/download/rosetta_5.82_powerpc-apple-darwin http://boinc.bakerlab.org/rosetta/download/rosetta_5.82_windows_intelx86.exe http://boinc.bakerlab.org/rosetta/download/rosetta_5.82_windows_x86_64.exe http://boinc.bakerlab.org/rosetta/download/rosetta_5.82_x86_64-pc-linux-gnu The current instructions are based on this application but will not work for some result formats. Yes I did, this was mentioned in previous threads, but this won't work.... Something about Rama_smooth_dyn.dat_ss_6.4 It would be very helpful to post new instructions.
31) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69418) Posted 18 Jan 2011 by Mike Post: I can look into it Tuesday. It shouldn't take that long but it likely will not work for all workunits. If you're an academic you can get a rosetta license, build the package, and use the score application for extracting pdbs. http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_scoring.html Are you going to update it tonight then
32) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69397) Posted 17 Jan 2011 by Mike Post: I'll update the instructions. It may be different with the various jobs using different protocols etc... How long will it take
33) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69396) Posted 17 Jan 2011 by Mike Post: How long is it expected to take
34) Message boards : Rosetta@home Science : ATTENTION: PLEASE SOLVE THIS ONGOING ISSUE (Message 69394) Posted 16 Jan 2011 by Mike Post: It has been painfully hard to find a way to view my predictions in PDB format by running a command line to convert a silent file to a pdb file on Windows.... This is very useful because PyMol can help view the alignment of my prediction to the native structure.... Yes, there is a page on how to view structure predictions, but the -extract command is no longer implemented.... There must be some other way, and I have been looking through the Rosetta Commons documentation but haven't found one yet.... PLEASE HELP ME WITH THIS!! This has been long unsolved -Michael D.
35) Message boards : Rosetta@home Science : Extracting .out files to make .pdb files. (Message 69304) Posted 14 Jan 2011 by Mike Post: Actually my method doesn't work but maybe you guys could help me with the documentation at rosetta commons for input output command line... http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/
36) Message boards : Rosetta@home Science : Extracting .out files to make .pdb files. (Message 68982) Posted 2 Jan 2011 by Mike Post: minirosetta_2.17_windows_intelx86.exe -in:file:silent default.out -out:pdb I love figuring these out
37) Message boards : Number crunching : Language used. (Message 66317) Posted 24 May 2010 by Mike Post: the graphics is openGL certainly
38) Message boards : Number crunching : Viewing Protein Structure (Message 66306) Posted 23 May 2010 by Mike Post: http://boinc.bakerlab.org/rosetta/rah_view_predictions.php
39) Message boards : Number crunching : Viewing Protein Structure (Message 66304) Posted 23 May 2010 by Mike Post: The Page on the website gave me instructions that did not work It created a blank file named BOINC_Lockfile and did nothing else when i ran the command line
40) Message boards : Number crunching : Viewing Active Work Units that you ARE NOT working on (Message 66303) Posted 23 May 2010 by Mike Post: I think Murisaki just bull's eyed what I was trying to ask Does anyone know how to do it though

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