- modeller_usage - salilab.org

residue selection
by Lixia Jin 30 May '07

30 May '07

I have two chains in my model: A chain has 324 residues. I want to modify only part of chain A (193-249) and chain B. How do I select the residues? Thanks!

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define residues
by Lixia Jin 30 May '07

30 May '07

When I use: self.patch(residue_type='DISU', residues=(self.residues['199'], self.residues['205'])) it works. When I use: self.patch(residue_type='DISU', residues=(self.residues ['199:G'], self.residues ['205:G'])) it gives me error information: KeyError: 'No such residue: 199:G' What might be wrong? Thanks! ------ Atila Iamarino wrote: > I'm interested in modeling a protein forcing disulfide bridges but my > protein has two chains. How do I set the residue in the .py file? > > # Redefine the special_patches routine to include the additional disulfides > # (this routine is empty by default): > class mymodel(automodel): > def special_patches(self, aln): > # A disulfide between residues 8 and 45: > self.patch(residue_type='DISU', residues=(self.residues['8'], > self.residues['45'])) That's straightforward - just include a chain ID (see http://salilab.org/modeller/9v1/manual/node153.html) For example, self.patch(residue_type='DISU', residues=(self.residues['8:A'], self.residues['45:A'])) Ben Webb, Modeller Caretaker

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ImportError: No module named automodel...
by matteo 30 May '07

30 May '07

hi! i've just installed modeller9v1 from the source code on a x386 pc... everything went fine, but as i run mod9v1 xxx.py, i get this message: Traceback (most recent call last): File "<string>", line 1, in ? File "/home/teo/_work/_m-i7/modeller.py", line 3, in ? from modeller.automodel import * # Load the automodel class ImportError: No module named automodel i'm just using the default script file, with the proper file name: # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:/home/teo/_work/_m-i7/' a = automodel(env, alnfile = 'm-i7.ali', # alignment filename knowns = '1f88', # codes of the templates sequence = 'm-i7') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling can anybody help me? many thanks matteo

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Including disulfide bonds
by Atila Iamarino 23 May '07

23 May '07

Hi all, I'm interested in modeling a protein forcing disulfide bridges but my protein has two chains. How do I set the residue in the .py file? # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class mymodel(automodel): def special_patches(self, aln): # A disulfide between residues 8 and 45: self.patch(residue_type='DISU', residues=(self.residues['8'], self.residues['45'])) -- Atila Iamarino L.E.M.B. - Laboratory of Molecular Evolution and Bioinformatics Av. Prof. Lineu Prestes, 1734 - USP (University of SÃ£o Paulo) - ICB Zip: 05508-000 Phone: +55 11 30917290 / +55 11 30918453

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disulfide
by Lixia Jin 17 May '07

17 May '07

Hi, First try MODELLER. It worked good. Then I added DISU as I learned from the manual by redefining the special_patches(). (Script as below) The new model is the same as the old one. I don't see disulfide bond between the two cysteins. Can any one explain it a bit? Thank you! Lixia ------------------ # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class #redefine the special_patches routine to include the additional disulfides #This routine is empty by default class mymodel(automodel): def special_patches(self, aln): # A disulfide between 199-205 self.patch(residue_type='DISU', residues=(self.residues['199'], self.residues['205'])) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:..' a = mymodel(env, alnfile = 'align2.ali', # alignment filename knowns = 'e791', # codes of the templates sequence = 'spnG') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make () # do the actual homology modeling

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model transmenbrane regions
by jinlian05＠lzu.cn 16 May '07

16 May '07

Hi: My template protein belongs to the GPCR family,I want to only use the transmembrane regions of the template,and i want to get only TM regions of target protein, but i dont know how to do. When i align my model sequence using its TM region with my template protein ,also using template's TM region, i get not the TM structure, it look likes the whole structure, please?

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use bovin rhodopsin as template
by jinlian05＠lzu.cn 16 May '07

16 May '07

Hi: I want to use MODELLER9v1 to model the protein 3D structure, it belongs to the GPCR family, I choose bovin rhodopsin as the template. I want to only use the transmember regions of the template, but i dont know how to restraints the template sequence.Or is there another method i can use, please? Thanks a lot!

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Making many result model
by 서주현 16 May '07

16 May '07

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Re: [modeller_usage] Ubuntu installation issue
by Modeller Caretaker 15 May '07

15 May '07

carromeu(a)usp.br wrote: > Hi Modellers, > > I'm trying to install Modeller on Ubuntu 7.04. I follow the steps from the Ben's > answer, but I don't do the symlink. In true, I don't know how to do this. Any > help is welcome. Making the symlink is easy: assuming you already have the RPM installed, just do (as root, and all on one line) ln -sf /usr/lib/modeller9v1/modlib/modeller /usr/lib/python2.5/site-packages/ 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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problems modeling a multimer
by Douglas Kojetin 15 May '07

15 May '07

Hi All, I would like create a hexameric model using a target sequence and a hexameric PDB template. I am trying to create an alignment using input files that have the \ character to separate the chains. Example: >P1;target sequence:target:::::::0.00: 0.00 AAAAA\ BBBBB\ CCCCC\ DDDDD\ EEEEE\ FFFFF* I'm using the align2d.py example, as detailed in tutorial 2. My input PDB file has six chains (A-F). My align2d.py file is as follows: """ align2d.py START from modeller import * log.verbose() env = environ() aln = alignment(env) mdl = model(env, file='PDBfile_hexamer', model_segment= ('FIRST:A','LAST:F')) aln.append_model(mdl, align_codes='PDBfile_hexamer', atom_files='PDBfile_hexamer.pdb') aln.append(file='target_hexamer.ali', align_codes='target') aln.align2d() aln.write(file='target_hexamer-PDBfile_hexamer.ali', alignment_format='PIR') aln.write(file='target_hexamer-PDBfile_hexamer.pap', alignment_format='PAP') """align2d.py END Using modeller9v1 (linux RPM), I started the above calculation (python align2d.py), but it has not finished after 20 hours (and is still going; 100% CPU and 22.6% memory usage out of 3 GB total, according to 'top'). Although I used log.verbose(), there is very little output in the associated log (see below). Any ideas? Thanks, Doug """ LOG START MODELLER 9v1, 2007/01/19, r4822 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2007 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 carbo.msbb.uc.edu 2.6.18-1.2869.fc6 i686 Date and time of compilation : 2007/01/19 13:47:34 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2007/05/11 11:26:27 openf___224_> Open $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL9v1}/modlib/ resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v1}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3216122 3140.744 3.067 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3216650 3141.260 3.068 openf___224_> Open ${MODINSTALL9v1}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3265250 3188.721 3.114 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 ${MODINSTALL9v1}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3280562 3203.674 3.129 openf___224_> Open ${MODINSTALL9v1}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v1}/modlib/solv.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL9v1}/modlib/ af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v1}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v1}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v1}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> model.read(file='PDBfile_hexamer', (def) model_format='PDB', model_segment=('FIRST:A', 'LAST:F')) openf___224_> Open PDBfile_hexamer.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 7756771 7574.972 7.397 openf___224_> Open PDBfile_hexamer.pdb read_mo_297_> Segments, residues, atoms: 24 4818 38574 read_mo_298_> Segment: 1 4 A 234 A 1790 read_mo_298_> Segment: 2 246 A 271 A 214 read_mo_298_> Segment: 3 291 A 636 A 2799 read_mo_298_> Segment: 4 651 A 850 A 1626 read_mo_298_> Segment: 5 4 B 234 B 1790 read_mo_298_> Segment: 6 246 B 271 B 214 read_mo_298_> Segment: 7 291 B 636 B 2799 read_mo_298_> Segment: 8 651 B 850 B 1626 read_mo_298_> Segment: 9 4 C 234 C 1790 read_mo_298_> Segment: 10 246 C 271 C 214 read_mo_298_> Segment: 11 291 C 636 C 2799 read_mo_298_> Segment: 12 651 C 850 C 1626 read_mo_298_> Segment: 13 4 D 234 D 1790 read_mo_298_> Segment: 14 246 D 271 D 214 read_mo_298_> Segment: 15 291 D 636 D 2799 read_mo_298_> Segment: 16 651 D 850 D 1626 read_mo_298_> Segment: 17 4 E 234 E 1790 read_mo_298_> Segment: 18 246 E 271 E 214 read_mo_298_> Segment: 19 291 E 636 E 2799 read_mo_298_> Segment: 20 651 E 850 E 1626 read_mo_298_> Segment: 21 4 F 234 F 1790 read_mo_298_> Segment: 22 246 F 271 F 214 read_mo_298_> Segment: 23 291 F 636 F 2799 read_mo_298_> Segment: 24 651 F 850 F 1626 relabel_387W> Model has multiple chains, and they do not all have a unique chain ID. Suggest you relabel them as A, B, C, etc. runcmd______> alignment.append_model (atom_files='PDBfile_hexamer.pdb', align_codes='PDBfile_hexamer') Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 7896464 7711.391 7.531 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 10639518 10390.154 10.147 runcmd______> alignment.append(align_codes=['PDBfile_hexamer', 'target'], atom_files=['PDBfile_hexamer.pdb'], file='target_hexamer.ali', (def)remove_gaps=True, (def) alignment_format='PIR', (def)rewind_file=False, (def)close_file=True) openf___224_> Open target_hexamer.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 12123550 11839.404 11.562 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 13607494 13288.568 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13607522 13288.596 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13607550 13288.623 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13607578 13288.650 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13607606 13288.678 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13607634 13288.705 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13627070 13307.686 12.996 Read the alignment from file : target_hexamer.ali Total number of alignment positions: 4865 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------ ------- 1 PDBfile_hexa 4818 24 PDBfile_hexame undefined 2 target 4860 6 target runcmd______> alignment.align2d((def)overhang=0, (def)align_block=0, (def)rr_file='$(LIB)/as1.sim.mat', (def)align_what='BLOCK', (def) off_diagonal=100, (def)max_gap_length=999999, (def) local_alignment=False, (def)matrix_offset=0.0, (def)gap_penalties_1d= (-900.0, -50.0), (def)gap_penalties_2d=(3.5, 3.5, 3.5, 0.20000000000000001, 4.0, 6.5, 2.0, 0.0, 0.0), (def)surftyp=1, (def) fit=True, (def)fix_offsets=(0.0, -1.0, -2.0, -3.0, -4.0), (def) read_weights=False, (def)write_weights=False, (def) input_weights_file='', (def)output_weights_file='', (def)n_subopt=1, (def)subopt_offset=0.0, (def)read_profile=False, (def) input_profile_file='', (def)write_profile=False, (def) output_profile_file='', (def)weigh_sequences=False, (def) smooth_prof_weight=10, (def)weights_type='SIMILAR') align2d_276_> 'align_block' changed to 1. openf___224_> Open PDBfile_hexamer.pdb Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 13627550 13308.154 12.996 openf___224_> Open PDBfile_hexamer.pdb mkapsa__637W> No residue topology library is in memory. Better radii would be used if topology.read() is called first. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 """ LOG END

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