- modeller_usage - salilab.org

PDF score question
by albert 02 Mar '12

02 Mar '12

Hello: As far as we know the lower DOPE score, the better model. I am wondering how about the PDF score? also the lower score, the better model? eg: model A PDF=200 is better than model B PDF score=300. I found that sometimes the PDF score can be negative such as: -20. Will this a good model? THX

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a 20 aa loop
by albert 02 Mar '12

02 Mar '12

Hello: I've got a 20 aa loop and I am wondering will the Loop refinement protocol in Modeller can handle such big loop? Is there any parameters can be refined to get more reliable model for such big loop? Thank you very much

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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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