- modeller_usage - salilab.org

Make model containing alpha-helix in addition to template
by Iain Aspley 10 Oct '12

10 Oct '12

Hello Modellers, I am having difficulty getting modeller to produce a model for my sequence containing a region which has no template which I wish to be an alpha-helix, the rest of the sequence should be modelled according to the template. I used the following script from modeller.automodel import* from modeller import* # Set up environment log.verbose() env=environ() env.libs.topology.read('${LIB}/top_heav.lib') env.libs.parameters.read('${LIB}/par.lib') env.io.atom_files_directory='./:../3BO9.pdb' a=automodel(env, alnfile='target2.ali', knowns='3BO9', sequence='query') a.restraints.add(secondary_structure.alpha(a.residue_range('129:A', '154:A'))) a.starting_model=1 a.ending_model=5 a.make() and I receive the following error messages Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "target2.py", line 14, in ? a.restraints.add(secondary_structure.alpha(a.residue_range('129:A', '154:A'))) File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 304, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 234, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9.10/modlib/modeller/util/modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9.10/modlib/modeller/coordinates.py", line 298, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 129:A' I have checked the pdb file and the residues do indeed exist! The log file reads as follows 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 bio-haw-pc10 2.6.32-43-generic x86_64 Date and time of compilation : 2011/09/28 18:39:17 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2012/10/10 11:28:47 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 ${LIB}/top_heav.lib read_to_681_> topology.submodel read from topology file: 3 openf___224_> Open ${MODINSTALL9v10}/modlib/models.lib openf___224_> Open ${LIB}/par.lib Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 4241404 4141.996 4.045 openf___224_> Open ${LIB}/par.lib read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE 227 561 661 112 0 io_data____W> Setting io.atom_files_directory to a colon-delimited string is deprecated, as it is not robust on Windows systems. Set it to a list of directories instead. For example: env.io.atom_files_directory = ['./', '../3BO9.pdb'] automodel__W> Topology and/or parameter libraries already in memory. These will be used instead of the automodel defaults. If this is not what you want, clear them before creating the automodel object with env.libs.topology.clear() and env.libs.parameters.clear() Can anybody help me please? Thanks in advance Iain Aspley

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No atoms were read from the specified input PDB file
by yael steuerman 10 Oct '12

10 Oct '12

Hello, I'm using thos PIR file: >P1;2ks9 structureX:2ks9:1 :A :364 : :::: MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWIILAHKRMRTVTNYFLVNLAFAEAS MAAFNTVVNFTYAVHN-EWYYGLFYCKFHNFFPIAAVFASIYSMTAVAFDRYMAIIHPLQPR--LSATATKVVICVIWVL ALLLAFPQGYYSTTETM-PSRVVCMIEWPEHP---------NKIYEKVYHICVTVLIYFLPLLVIGYAYTVVGITLWASE IPGDSSDRYHEQVSAKRKVVKMMIVVVCTFAICWLPFHIFFLLPYINPDLYLKK---FIQQVYLAIMWLAMSSTMYNPII YCCLNDRFRLGFKHAFRCCPFISAGDYEGLEMKSTRYLQTQGSVYKVSR* >P1;FPR1 sequence:FPR1:1 : :350 : :::: METNSSL------PTNISGGTPAVSAGYLFLDIITYLVFAVTFVLGVLGNGLVIWVAGFRMT-HTVTTISYLNLAVADFC F-TSTLPFFMVRKAMGGHWPFGWFLCKFVFTIVDINLFGSVFLIALIALDRCVCVLHPVWTQNHRTVSLAKKVIIGPWVM ALLLTLPVIIRVTTVPGKTGTVACTFNFSPWTNDPKERINVAVAMLTVRGIIRFIIGFSAPMSIVAVSYGLIATKIHKQG ------------LIKSSRPLRVLSFVAAAFFLCWSPYQVVALIATVRIRELLQGMYKEIGIAVDVTSALAFFNSCLNPML YVFMGQDFRERLIHALPASLERALTEDSTQTSDTATNSTLPSAEVELQA* ***The file 2ks9.pdb is exactly as I downloaded it from RCSB.. then I'm running the script: from modeller import * from modeller.automodel import * env = environ() a = automodel(env, alnfile='alnPrev.pir', knowns='2ks9', sequence='FPR1', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1 a.make() I can't seem to understand why do I get the following error: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 1", chain " A"; atom file name: 2ks9.pdb read_te_288W> Protein not accepted: 1 2ks9 It seems like it can't find residue number 1 but I think I can see it.. And when I'm changing the PIR file in the structure line from 1 to first I get the following error: read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 1) Alignment MDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWI PDB DNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWII Match ** * * ** * Alignment residue type 11 (M, MET) does not match pdb residue type 3 (D, ASP), for align code 2ks9 (atom file 2ks9), pdb residue number "2", chain "A" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 2ks9 What am I missing? The beggining of the ATOM part in the PDB file: MODEL 1 ATOM 1 N ASP A 2 -17.531 -22.009 -19.661 1.00 97.08 N ATOM 2 CA ASP A 2 -17.664 -21.563 -18.309 1.00 97.08 C ATOM 3 C ASP A 2 -17.647 -20.070 -18.302 1.00 97.08 C ATOM 4 O ASP A 2 -18.309 -19.432 -17.485 1.00 97.08 O ATOM 5 CB ASP A 2 -16.522 -22.041 -17.395 1.00 97.08 C ATOM 6 CG ASP A 2 -15.222 -21.430 -17.892 1.00 97.08 C ATOM 7 OD1 ASP A 2 -15.049 -21.341 -19.136 1.00 97.08 O ATOM 8 OD2 ASP A 2 -14.389 -21.037 -17.033 1.00 97.08 O ATOM 9 H ASP A 2 -16.684 -22.502 -19.945 1.00 0.00 H ATOM 10 HA ASP A 2 -18.637 -21.921 -17.898 1.00 0.00 H ATOM 11 HB2 ASP A 2 -16.714 -21.822 -16.319 1.00 0.00 H ATOM 12 HB3 ASP A 2 -16.471 -23.152 -17.318 1.00 0.00 H ATOM 13 N ASN A 3 -16.889 -19.477 -19.238 1.00123.41 N Thanks, Yael.

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Regarding the Modelling Utility
by Ashish Runthala 01 Oct '12

01 Oct '12

Dear Modellers, Is there a way that i can switch on the Steepest_Descent or Conjugated_Gradient (i.e. SD or CG) in the modelling script? More specifically, is there any option like env.io.sd=true or env.io.cg=true. So for the sampling or building up the desired set of models, it uses the considered option only. Best, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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modeller 9.11 and Ubuntu 12.04 installation
by Mike WA8BXN 28 Sep '12

28 Sep '12

from modeller import * line in scripts fails with ImportError: No module name modeller I have tried variations of the ln commands shown in the installation guide for Ubuntu 8 substituting 2.7 for the python version but still get the error message when trying to run the samples with command lines beginning with mod9.11 or python followed by the sample script file name. I've looked over archived messages and have been unable to find a solution to this problem. I would appreciate anyone that has installed modeller 9.11 on ubuntu 12.04 successfully telling me what particularly I need to do to make it work. The installation of modeller itself seems to have gone ok as the modeller files seem to be installed. Thanks! Mike

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mismatch in the alignment
by Sajeewa Pemasinghe 25 Sep '12

25 Sep '12

Hi, I am working on the 1qg8 example given at http://salilab.org/modeller/wiki/Missing%20residues. I am trying to read the HETATM records and the waters. Here is my alignment file. >P1;1qg8 structureX:1qg8: 2 :A:+661 :A:MOL_ID 1; MOLECULE SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA; CHAIN A; ENGINEERED YES; OTHER_DETAILS GLYCEROL MAGNESIUM:MOL_ID 1; ORGANISM_SCIENTIFIC BACILLUS SUBTILIS; GENE SPSA; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_STRAIN BL 21: 1.50: 0.16 PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTW NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT--------- -----EFVRNLPPQRNCRELRESLKKLGMG...wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww www* >P1;1qg8_fill sequence::::::::: PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTW NAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLF ELEKNEFVRNLPPQRNCRELRESLKKLGMG...wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww www* I have run the python script and get an error like this. Read the alignment from file : 1qg8.ali Total number of alignment positions: 678 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1qg8 661 1 1qg8 MOL_ID 1; MOLECULE SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA; CHAIN 2 1qg8_fill 678 1 check_a_343_> >> BEGINNING OF COMMAND openf___224_> Open .\1qg8.pdb Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 805668 786.785 0.768 read_pd_459W> Residue type GOL not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib. read_te_290E> Number of residues in the alignment and pdb files are different: 661 637 For alignment entry: 1 1qg8 x (mismatch at alignment position 638) Alignment wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww PDB wwwwwwwwwwwwwwwwwwww Match ******************** Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 1qg8 The pdb file has 661 residues and 17 are missing. To read the hetatm records I have used '.' and for the waters I have used 'w'. Could you please tell me where I have gone wrong? Thank you very much Sajeewa Dewage

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Reg :Error message: not able to open file
by Nanda Pandey 25 Sep '12

25 Sep '12

Hi, I am trying to do a simple modelling similar to the basic tutorial given in modeller website. I have converted my sequence to PIR format and have kept all files including the pdb database file in same directory but when i run the script build_profile.py, I am getting the following error : "cannot open file filename.ali: no such file or directory" To check the problem i tried repeating the same exercise as basic tutorial with TvLDH.ali but still getting same error. Please let me know what am I doing wrong. Thanks, Nanda.

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Reading in water residues
by Sajeewa Pemasinghe 25 Sep '12

25 Sep '12

Hi everyone, I want to read in hydrogens, heteroatoms and water molecules into my modeller-modeled protein structure. In the manual it says: to read in the heteroatoms, put env.io.hetatm=true and to use '.' characters in the alignment sequences. to read in the waters, put env.io.water=true and to use 'w' characters in the alignment sequences. Usually in a pdb file the 'ligand' heteroatoms are given as HETATM 843 FE1 SF4 A 107 14.698 20.785 10.230 1.00 13.78 FE and waters are given as HETATM 858 O HOH A 109 23.833 10.228 18.799 1.00 17.80 O so both of them use 'HETATM' . So my question is if we have asked the modeller to read ALL HETATM records by setting env.io.hetatm=true, do we have to specifically say again, to add waters by env.io.water=true. Can't we just read all the heteroatom records (including waters) and use '.' for both normal heteroatoms and waters? Thank you Sajeewa Dewage

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meaning of "env.io.atom_files_directory"
by Sajeewa Pemasinghe 22 Sep '12

22 Sep '12

Hi everyone, I am working on the tutorial in http://salilab.org/modeller/wiki/Missing%20residues. I have my pdb files in C:\Users\Sajeewa\Desktop\protease_project\modeller_practice directory. In the script to generate the model with all residues # directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files'] should this be changed as env.io.atom_files_directory = ['C:/Users/Sajeewa/Desktop/protease_project/modeller_practice'] ? I don't understand what it means by '.', '../atom_files' Could you please explain? Thank you Sajeewa Dewage

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sequence file produced is different from the one shown in the tutorial
by Sajeewa Pemasinghe 21 Sep '12

21 Sep '12

Hi everyone, I am working on the example given in the modeller tutorial http://salilab.org/modeller/wiki/Missing%20residues. I used the exact same script to generate the sequence file. Instead of the given pdb1qg8.ent , I used the 1qg8.pdb downloaded from www.rcsb.org. When I ran the script it resulted in the following sequence file (1qg8.seq) >P1;1qg8 structureX:1qg8: 2 :A:+238 :A:MOL_ID 1; MOLECULE SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA; CHAIN A; ENGINEERED YES; OTHER_DETAILS GLYCEROL MAGNESIUM:MOL_ID 1; ORGANISM_SCIENTIFIC BACILLUS SUBTILIS; GENE SPSA; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_STRAIN BL 21: 1.50: 0.16 PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTR YAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNDIVKETVRPAAQVTWNAP CAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITEFVRNLPPQRNC RELRESLKKLGMG* In the field 5, it says +238 whereas in the tutorial, in the resulting 1qg8.seq file it shows 256. Have I done any mistake? Would the above sequence file work just as fine as the one shown in the tutorial? Thank you Sajeewa Dewage

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Fwd: PIR file format
by Nanda Pandey 21 Sep '12

21 Sep '12

Thanks for the reply, Troubling you with one more query though.... "PIR files are just plain text, so they're very easy to make manually in a text editor or with some simple scripting." I have read in the forum that one needs to input PDB structure details also while changing the format, Please let me know if this is required for query sequence also or only while submitting the alignment as input (changed to PIR). Thanks and Regards, Nanda On Fri, Sep 21, 2012 at 6:00 PM, Modeller Caretaker < modeller-care(a)salilab.org> wrote: > On 9/21/12 6:26 AM, Nanda Pandey wrote: > >> Do i need to convert my sequence to PIR file format in order to use it. >> > > If by "use it", you mean you want to build a comparative model, then yes. > > > If yes, how do i do it?? >> > > PIR files are just plain text, so they're very easy to make manually in a > text editor or with some simple scripting. > > > Is it recommended to generate alignment from external sources and then >> perform modelling using modeller or I can generate my model for a >> sequence using only modeller. >> > > You can do it either way. The alignment you use for modeling doesn't have > to be generated by Modeller. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/**modeller/<http://www.salilab.org/modeller/> > Modeller mail list: http://salilab.org/mailman/**listinfo/modeller_usage<http://salilab.org/mailman/listinfo/modeller_usage> >

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