February 2012 - modeller_usage

Error: Ran out of slaves to run tasks
by Xiao-Ping Zhang 16 May '12

16 May '12

Dear Modellers, When I was refining loops for a model in parallel, I asked modeller to generate 9999 models. But modeller stopped at 1245 with the following error. The computer has six cores, modeller uses four of them. The other two cores were free. Thank you for your help. <Slave on localhost> failed (Connection lost to slave <Slave on localhost>: [Errno 104] Connection reset by peer) - removing from <Parallel job [<Slave on localhost>, <Slave on localhost>, <Slave on localhost>, <Slave on localhost>]> <Loop model building task #1.1219> on <Slave on localhost> completed <Loop model building task #1.1217> on <Slave on localhost> completed <Loop model building task #1.1222> on <Slave on localhost> completed <Loop model building task #1.1218> on <Slave on localhost> completed <Loop model building task #1.1223> on <Slave on localhost> completed <Loop model building task #1.1224> on <Slave on localhost> completed <Loop model building task #1.1225> on <Slave on localhost> completed <Loop model building task #1.1226> on <Slave on localhost> completed <Loop model building task #1.1228> on <Slave on localhost> completed <Loop model building task #1.1229> on <Slave on localhost> completed <Slave on localhost> failed (Connection lost to slave <Slave on localhost>: [Errno 104] Connection reset by peer) - removing from <Parallel job [<Slave on localhost>, <Slave on localhost>, <Slave on localhost>, <Slave on localhost>]> <Loop model building task #1.1227> on <Slave on localhost> completed <Loop model building task #1.1230> on <Slave on localhost> completed <Loop model building task #1.1232> on <Slave on localhost> completed <Loop model building task #1.1233> on <Slave on localhost> completed <Loop model building task #1.1234> on <Slave on localhost> completed <Slave on localhost> failed (Connection lost to slave <Slave on localhost>: [Errno 104] Connection reset by peer) - removing from <Parallel job [<Slave on localhost>, <Slave on localhost>, <Slave on localhost>, <Slave on localhost>]> <Loop model building task #1.1235> on <Slave on localhost> completed <Loop model building task #1.1237> on <Slave on localhost> completed <Loop model building task #1.1238> on <Slave on localhost> completed <Loop model building task #1.1239> on <Slave on localhost> completed <Loop model building task #1.1240> on <Slave on localhost> completed <Loop model building task #1.1241> on <Slave on localhost> completed <Loop model building task #1.1242> on <Slave on localhost> completed <Loop model building task #1.1243> on <Slave on localhost> completed <Loop model building task #1.1244> on <Slave on localhost> completed <Loop model building task #1.1245> on <Slave on localhost> completed <Slave on localhost> failed (Connection lost to slave <Slave on localhost>: [Errno 104] Connection reset by peer) - removing from <Parallel job [<Slave on localhost>, <Slave on localhost>, <Slave on localhost>, <Slave on localhost>]> Traceback (most recent call last): File "refine_loop.py", line 41, in <module> a.make() File "/usr/local/lib/python2.7/site-packages/modeller/automodel/loopmodel.py", line 36, in make self.build_seq(self.inimodel, 1) File "/usr/local/lib/python2.7/site-packages/modeller/automodel/loopmodel.py", line 190, in build_seq self.parallel_loop_models(atmsel, ini_model, num, sched) File "/usr/local/lib/python2.7/site-packages/modeller/automodel/loopmodel.py", line 208, in parallel_loop_models self.loop.outputs.extend(job.run_all_tasks()) File "/usr/local/lib/python2.7/site-packages/modeller/parallel/job.py", line 136, in run_all_tasks raise ValueError("Ran out of slaves to run tasks") ValueError: Ran out of slaves to run tasks XP

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a question about loop refinement
by mircial＠sjtu.edu.cn 29 Feb '12

29 Feb '12

Dear All: I am a new user of the MODELLER package. I am using the modeller package to refine a loop region of a X-ray crystal structure. I have finished modelling 100 independent structures of that loop and in order to pick out the "good" structures, I need to do cluster analysis on these structures and then compare the representative models from each cluster, am I right? My question is, could MODELLER package do this cluster analysis on the loop structures I got? or I need other softwares to do this analysis? Thanks in advance! R-X Gu

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Re: [modeller_usage] Error running build_profile.py :Not enough bins in histogram
by Susana Tomasio 29 Feb '12

29 Feb '12

> > Dear Modeller users, > > I am trying to search for the best template for my target molecule, and > therefore I created a file in PIR format with my sequences and then > I ran build_profile.py. I got the following error in my log file: > > > MODELLER 9.10, 2011/09/28, r8346 > > PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS > > > Copyright(c) 1989-2011 Andrej Sali > All Rights Reserved > > Written by A. Sali > with help from > B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, > N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, > R. Sanchez, B. Yerkovich, A. Badretdinov, > F. Melo, J.P. Overington, E. Feyfant > University of California, San Francisco, USA > Rockefeller University, New York, USA > Harvard University, Cambridge, USA > Imperial Cancer Research Fund, London, UK > Birkbeck College, University of London, London, UK > > > Kind, OS, HostName, Kernel, Processor: 4, Linux pan 3.0.0-12-generic x86_64 > Date and time of compilation : 2011/09/28 17:58:44 > MODELLER executable type : x86_64-intel8 > Job starting time (YY/MM/DD HH:MM:SS): 2012/02/29 16:37:57 > > openf___224_> Open $(LIB)/restyp.lib > openf___224_> Open ${MODINSTALL9v10}/modlib/resgrp.lib > rdresgr_266_> Number of residue groups: 2 > openf___224_> Open ${MODINSTALL9v10}/modlib/sstruc.lib > > Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 > 3158.277 3.084 > > Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 > 3158.793 3.085 > openf___224_> Open ${MODINSTALL9v10}/modlib/resdih.lib > > Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 > 3206.254 3.131 > rdrdih__263_> Number of dihedral angle types : 9 > Maximal number of dihedral angle optima: 3 > Dihedral angle names : Alph Phi Psi Omeg > chi1 chi2 chi3 chi4 chi5 > openf___224_> Open ${MODINSTALL9v10}/modlib/radii.lib > > Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 > 3215.277 3.140 > openf___224_> Open ${MODINSTALL9v10}/modlib/radii14.lib > openf___224_> Open ${MODINSTALL9v10}/modlib/af_mnchdef.lib > rdwilmo_274_> Mainchain residue conformation classes: APBLE > openf___224_> Open ${MODINSTALL9v10}/modlib/mnch.lib > rdclass_257_> Number of classes: 5 > openf___224_> Open ${MODINSTALL9v10}/modlib/mnch1.lib > openf___224_> Open ${MODINSTALL9v10}/modlib/mnch2.lib > openf___224_> Open ${MODINSTALL9v10}/modlib/mnch3.lib > openf___224_> Open ${MODINSTALL9v10}/modlib/xs4.mat > rdrrwgh_268_> Number of residue types: 21 > openf___224_> Open pdb.pir > > Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 3293057 > 3215.876 3.141 > > Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3294891 > 3217.667 3.142 > > Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3296341 > 3219.083 3.144 > > Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3299241 > 3221.915 3.146 > > Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3305041 > 3227.579 3.152 > > Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]: 3310040 > 3232.461 3.157 > > SEQ_DATABASE_FILE : pdb.pir > SEQ_DATABASE_FORMAT : PIR > CHAINS_LIST : ALL > CLEAN_SEQUENCES : T > MINMAX_DB_SEQ_LEN : 30 4000 > Number of sequences : 4 > Number of residues : 1060 > Length of longest sequence: 271 > > > SEQ_DATABASE_FILE : pdb_3.bin > SEQ_DATABASE_FORMAT : BINARY > SEARCH_CHAINS_LIST : ALL > Number of sequences : 4 > Number of residues : 1060 > Length of longest sequence: 271 > > > SEQ_DATABASE_FILE : pdb_3.bin > SEQ_DATABASE_FORMAT : BINARY > CHAINS_LIST : ALL > CLEAN_SEQUENCES : T > MINMAX_DB_SEQ_LEN : 0 999999 > Number of sequences : 4 > Number of residues : 1060 > Length of longest sequence: 271 > > openf___224_> Open chst11.ali > > Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3300046 > 3222.701 3.147 > > Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3301496 > 3224.117 3.149 > > Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3304396 > 3226.949 3.151 > > Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3310196 > 3232.613 3.157 > > Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3311600 > 3233.984 3.158 > > Read the alignment from file : chst11.ali > Total number of alignment positions: 352 > > # Code #_Res #_Segm PDB_code Name > > ------------------------------------------------------------------------------- > 1 chst11 352 1 chst11 > > Dynamically allocated memory at amaxprofile [B,KiB,MiB]: 3313325 > 3235.669 3.160 > openf___224_> Open ${LIB}/blosum62.sim.mat > rdrrwgh_268_> Number of residue types: 21 > profile_iteration_> processing sequence: 1 352 1 > 0.0100000 0.0100000 0.0100000 1 > regress_657E> Not enough bins in histogram - cannot calculate statistics, > nbins: 1 > > My build_profile.py file is the following: > > from modeller import * > > log.verbose() > env = environ() > > #-- Prepare the input files > > #-- Read in the sequence database > sdb = sequence_db(env) > sdb.read(seq_database_file='pdb.pir', seq_database_format='PIR', > chains_list='ALL', minmax_db_seq_len=(30, 4000), > clean_sequences=True) > > #-- Write the sequence database in binary form > sdb.write(seq_database_file='pdb_3.bin', seq_database_format='BINARY', > chains_list='ALL') > > #-- Now, read in the binary database > sdb.read(seq_database_file='pdb_3.bin', seq_database_format='BINARY', > chains_list='ALL') > > #-- Read in the target sequence/alignment > aln = alignment(env) > aln.append(file='chst11.ali', alignment_format='PIR', align_codes='ALL') > > #-- Convert the input sequence/alignment into > # profile format > prf = aln.to_profile() > > #-- Scan sequence database to pick up homologous sequences > prf.build(sdb, matrix_offset=-450, rr_file='${LIB}/blosum62.sim.mat', > gap_penalties_1d=(-500, -50), n_prof_iterations=10, > check_profile=True, max_aln_evalue=0.01) > > #-- Write out the profile in text format > prf.write(file='build_profile.prf', profile_format='TEXT') > > #-- Convert the profile back to alignment format > aln = prf.to_alignment() > > #-- Write out the alignment file > aln.write(file='build_profile.ali', alignment_format='PIR') > > If anyone could help me with this I would be grateful. > > Many thanks in advance, > > Susana > >

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Special g
by zhoujinming 26 Feb '12

26 Feb '12

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(no subject)
by ARVIND PAL 21 Feb '12

21 Feb '12

After runing of optimize.py. what i can interpret from the log file.

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Re: [modeller_usage] How to use MODELLER as an ordinary Python module?
by Modeller Caretaker 21 Feb '12

21 Feb '12

On 2/21/12 7:34 AM, Desmond Kho wrote: > I had tried /python plot_profiles.py/ but nothing seem to be happen. > No file was generated. > Following was the only log shown in the cmd prompt before it stop. > > MODELLER 9.9, 2011/03/29, r7963 > > PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS OK, the fact that you're seeing the Modeller header means that everything is working correctly. I don't know why you're not seeing any output files - perhaps you're looking in the wrong place for them - but you would see an error message if something went wrong. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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How to use MODELLER as an ordinary Python module?
by Desmond Kho 21 Feb '12

21 Feb '12

Hi, I have problem with ' 'import site' failed' when I run plot_profiles.py script. File "plot_profiles.py", line 1, in ? import pylab ImportError: No module named pylab I have all Python2.6, Matplodlib, NumPy, SciPy installed. I read about "Known issues and questions with 9.10", but can't find the instructions for running Modeller with Python. May I know how to run Modeller with pyhton beside the mod9.10 script? Thanks.

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energy function scaling factors
by Armin Meier 20 Feb '12

20 Feb '12

Hi Modellers, MODELLER provides a scaling option for energy function terms via e.g.: env.schedule_scale=physical.values(default=1.0, ca_distance=2) In this case, ca_distances are upscaled. If a CA-CA distance is described by a single Gaussian, its restraint is as in http://salilab.org/modeller/manual/node469.html#SECTION001332100000000000000 When scaling CA-CA distances by factor 2, is then "c" (and dc/df) simply multiplied by 2? Thanks for elucidation

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Confusion between two models
by hari krishna 19 Feb '12

19 Feb '12

Dear All, I am trying to model a protein containing 859 amino acids. After loop modeling and refinement of two different models, I have doubt in chosing which model for further usage.. Becuase the stereochemical quality was good for one model (85% in favorable region) and for the second model its about 65%. Except this all other parameters like Z-score, energy, residue error plot and DOPE score favors the second model. In this case which one i need to choose. Please help me in this regard. I am attaching the procheck program results. Also the second model superimpose well to their homology proteins compared to the first model MODEL 1 +----------<<>>----------+ | | | input_atom_only.pdb 2.5 858 residues | | | *| Ramachandran plot: 85.4% core 11.4% allow 2.1% gener 1.1% disall | | | *| All Ramachandrans: 49 labelled residues (out of 854) | +| Chi1-chi2 plots: 5 labelled residues (out of 502) | | Main-chain params: 6 better 0 inside 0 worse | | Side-chain params: 5 better 0 inside 0 worse | | | *| Residue properties: Max.deviation: 15.7 Bad contacts: 57 | *| Bond len/angle: 10.7 Morris et al class: 1 1 3 | | | | G-factors Dihedrals: -0.07 Covalent: -0.36 Overall: -0.18 | | | | M/c bond lengths: 97.8% within limits 2.2% highlighted | *| M/c bond angles: 90.5% within limits 9.5% highlighted 1 off graph | | Planar groups: 100.0% within limits 0.0% highlighted | | | +----------------------------------------------------------------------------+ + May be worth investigating further. * Worth investigating further. MODEL 2 +----------<<>>----------+ | | | input_atom_only.pdb 2.5 859 residues | | | *| Ramachandran plot: 64.7% core 28.0% allow 4.6% gener 2.7% disall | | | *| All Ramachandrans: 147 labelled residues (out of 825) | *| Chi1-chi2 plots: 16 labelled residues (out of 472) | +| Main-chain params: 4 better 0 inside 2 worse | | Side-chain params: 5 better 0 inside 0 worse | | | *| Residue properties: Max.deviation: 9.3 Bad contacts: 0 | *| Bond len/angle: 7.1 Morris et al class: 3 2 2 | *| 5 cis-peptides | +| G-factors Dihedrals: -0.90 Covalent: -0.13 Overall: -0.57 | | | | M/c bond lengths:100.0% within limits 0.0% highlighted | | M/c bond angles: 90.2% within limits 9.8% highlighted | *| Planar groups: 57.1% within limits 42.9% highlighted 69 off graph | | | +----------------------------------------------------------------------------+ + May be worth investigating further. * Worth investigating further. S.Harikrishna

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loop error
by albert 19 Feb '12

19 Feb '12

Hello: I am trying to generate loop models with loop protocol in the latest Modeller verison. It only produced 8 models and stopped, and it said the following: File "loop.py", line 41, in <module> a.make() File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 36, in make self.build_seq(self.inimodel, 1) File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 190, in build_seq self.parallel_loop_models(atmsel, ini_model, num, sched) File "/usr/lib64/python2.7/site-packages/modeller/automodel/loopmodel.py", line 208, in parallel_loop_models self.loop.outputs.extend(job.run_all_tasks()) File "/usr/lib64/python2.7/site-packages/modeller/parallel/job.py", line 131, in run_all_tasks for task in self._finish_all_tasks(): File "/usr/lib64/python2.7/site-packages/modeller/parallel/job.py", line 164, in _finish_all_tasks task = self._process_event(obj, s) File "/usr/lib64/python2.7/site-packages/modeller/parallel/job.py", line 180, in _process_event task = obj.task_results() File "/usr/lib64/python2.7/site-packages/modeller/parallel/slave.py", line 61, in task_results r = self.get_data(allow_heartbeat=True) File "/usr/lib64/python2.7/site-packages/modeller/parallel/communicator.py", line 89, in get_data (cmdtype, obj) = self._recv() File "/usr/lib64/python2.7/site-packages/modeller/parallel/communicator.py", line 130, in _recv raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: <type 'ValueError'>: GA341______E> Sequence identity -999.000 out of range - must be between 0 and 100. Seq. ID is read from the model.seq_id variable, which is obtained automatically from the REMARK lines of MODELLER-produced PDB files from <Slave on localhost>

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