- modeller_usage - salilab.org

Template selection criteria.
by ARVIND PAL 01 Mar '12

01 Mar '12

I am a new user of the MODELLER package. Plz tell me what is criteria for template selection.

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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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