June 2007 - modeller_usage

model.energy()
by Jayapal, Prabha 27 Jun '07

27 Jun '07

Dear All: I am a new user of MODELLER 9. I got an appreciable model using modeller and I would like to evaluate the model by the model.energy(). But I got an error like, runcmd______> topology.append(file='$(LIB)/top_heav.lib') read_to_681_> topology.submodel read from topology file: 3 runcmd______> parameters.append(file='$(LIB)/par.lib') runcmd______> model.read(file='nitro.B99990066', (def)model_format='PDB', (def)model_segment=('FIRST:@', 'LAST:')) runcmd______> alignment.append_model(atom_files='nitro.B99990066', align_codes='nitro.B99990066') runcmd______> alignment.append_model(atom_files='nitro.B99990066.ini', align_codes='nitro.B99990066-ini') runcmd______> model.generate_topology((def)patch_default=True) getf_______W> RTF restraint not found in the atoms list: residue type, indices: 11 120 atom names : C +N atom indices : 880 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 11 120 atom names : C CA +N O atom indices : 880 875 0 881 runcmd______> model.transfer_xyz((def)cluster_cut=-1.0, (def)cluster_method='RMSD') transfe_507E> Number of residues in alignment different from that in MODEL: 60 120 (Did you call clear_topology() before generate_topology() ?) The top file is, # Example for: model.energy() # This will calculate the stereochemical energy (bonds, # angles, dihedrals, impropers) for a given model. env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') aln = alignment(env) code = "nitro.B99990066" mdl = model(env, file=code) aln.append_model(mdl, atom_files=code, align_codes=code) aln.append_model(mdl, atom_files=code+'.ini', align_codes=code+'-ini') mdl.generate_topology(aln[code+'-ini']) mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False) molpdf = mdl.energy(edat=energy_data(dynamic_sphere=True)) Could any body help me with this? I used PROCHECK and found 90% of residue resides in core area ie most favoured. Thank you in advance Cheers J.Prabha

2 1

Sequence alignment softwares
by DPF Chocolate 26 Jun '07

26 Jun '07

Hi, I have got some exprience on modeller using InsightII software. I used to do sequence alignment using InsightII software. If I want to do sequence alignment without InsightII, how can I do that. Are there any free sequence alignment softwares (GUI) available, so that we can save ".pir" file and give that file to modeller. -- Regards, JOCKY

1 0

homology problem
by Fabian Glaser 14 Jun '07

14 Jun '07

Hello all, I am recently became interested in modeling, and I am trying to model a recently discovered protein, that unfortunately appears not to have homologues at all. I tried to run the molecule domain by domain, try to use GenTHREADER, 3DPSSM and several others methods and metaservers to find homologues, but nothing gives an alignment with a reasonable accuracy or p-value. Could somebody recommend me what to do in this case to obtain a reasonable alignment / model? Any suggestion will be highly appreciated. Best regards, Fabian Glaser, PhD Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology Haifa 32000, ISRAEL E-mail: *fglaser(a)tx.technion.ac.il* <fglaser(a)tx.technion.ac.il> Tel: +972-4-829-3701

1 0

help--model-segment.py
by jinlian05＠lzu.cn 06 Jun '07

06 Jun '07

Hi: I use 'model-segment.py' to build the structure of my target protein, the following is the script: from modeller import * from modeller.automodel import * log.verbose() class mymodel(automodel): def select_atoms(mdl): return selection(mdl.residue_range('37:A','63:A'), mdl.residue_range('74:A','96:A'), mdl.residue_range('111:A','133:A'), mdl.residue_range('153:A','173:A'), mdl.residue_range('203:A','224:A'), mdl.residue_range('250:A','274:A'), mdl.residue_range('287:A','308:A')) env=environ() env.io.atoms_files_directory='./:../atom_files' env.edat.nonbonded_sel_atoms=2 a=mymodel(env, alnfile='1u19-tm.ali', knowns='1u19', sequence='mrg-tm') a.starting_model=1 a.ending_model=1 a.make() after running the scripts, it appears some errors: Traceback (most recent call last): File "selection.py", line 22, in ? a.make() File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 118, in make atmsel = self._check_select_atoms() File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 483, in _check_select_atoms atmsel = self.select_atoms() File "selection.py", line 6, in select_atoms return selection(mdl.residue_range('37:A','63:A'), File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 64, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 165, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v1/modlib/modeller/util/modutil.py", line 76, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 50, in _indxres raise KeyError, ("No such residue: %s" % indx) KeyError: 'No such residue: 37:A' The residue numbers in the model are really the same as residue numbers in the template. After 'mod9v1 model-segment.py', it produce the 'tm-mrg.ini' and 'tm-mrg.scr'files, if the script is wrong, dose it produce results else? ps: is there any diffference between the .ini files and .pdb files?

2 1

modweb
by James Fethiere 05 Jun '07

05 Jun '07

Hi, is there a way to tell modweb to use a specific pdb as template instead of the one he finds by itself. Thanks james

1 0

model-multiple.py error
by Eeson Rajendra 05 Jun '07

05 Jun '07

Hi there I am building a structure from 12 high-resolution crystal structures of high (>75%) sequence homology. When I run model-multiple.py I get the following error: ******************* >mod9v1 model- multiple.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "model-multiple.py", line 35, in ? a.make() # do the actual homology modeling File "C:\Program Files\Modeller9v1\modlib\modeller\automodel\automodel.py", li ne 108, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller9v1\modlib\modeller\automodel\automodel.py", li ne 403, in homcsr aln = self.read_alignment() File "C:\Program Files\Modeller9v1\modlib\modeller\automodel\automodel.py", li ne 397, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "C:\Program Files\Modeller9v1\modlib\modeller\alignment.py", line 76, in append io=io.modpt, libs=self.env.libs.modpt, File "C:\Program Files\Modeller9v1\modlib\modeller\io_data.py", line 35, in __ get_modpt self.atom_files_directory) TypeError: in method 'set_io_data', argument 5 of type 'char const *' ********************************* Any help would be appreciated! Best regards, Eeson -- Eeson Rajendra

2 3

help--model-segment.py
by jinlian05＠lzu.cn 04 Jun '07

04 Jun '07

Hi: My target protein is GPCR, I use bovin rhodopsin as template.And, I alignment the transmenbrane regions between template and target protein.I build model using the fllowing scripts: from modeller import * from modeller.automodel import * log.verbose() class mymodel(automodel): def select_atoms(self): return selection(self.residue_range('37:A','63:A'), self.residue_range('74:A','96:A'), self.residue_range('111:A','133:A'), self.residue_range('153:A','173:A'), self.residue_range('203:A','224:A'), self.residue_range('250:A','274:A'), self.residue_range('287:A','308:A')) env=environ() env.io.atoms_files_directory='./:../atom_files' env.edat.nonbonded_sel_atoms=2 a=mymodel(env, alnfile='1u19-tm.ali', knowns='1u19', sequence='mrg-tm') a.starting_model=1 a.ending_model=1 a.make() But there are some errors: Traceback (most recent call last): File "selection.py", line 23, in ? a.make() File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 118, in make atmsel = self._check_select_atoms() File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 483, in _check_select_atoms atmsel = self.select_atoms() File "selection.py", line 6, in select_atoms return selection(self.residue_range('37:A','63:A'), File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 64, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 165, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v1/modlib/modeller/util/modutil.py", line 76, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 50, in _indxres raise KeyError, ("No such residue: %s" % indx) KeyError: 'No such residue: 37:A' How to repair the script? The following is alignment file: >P1;1u19 structureX:1u19: 1 :A:+348 :A:undefined:undefined:-1.00:-1.00 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQ--- FSMLAAYMFLLIMLGFPINFLTLYVTV QHKKLRTPLN --YILLNLAVADLFMVFGGFTTTLY TSLHGYFVFGPTGC-- NLEG--FFATLGGEIALWSLVVLAI ---ERYVVVCKPMSNFRFGENH --AIMGVAFTWVMALACAAPPLV GWSRYIPEGMQCSCGIDYYTPHEETNNES FVIYMFVVHFIIPLI---VIFFCYG QLVFTVKEAAAQQQESATTQKAEKE VTRMVIIMVIAFLICWLPYAGVAFY ----IFTHQGSDFGPI- FMTIPAFFAKTSAVYNPVIYIM- -------MNKQFRNCMVTTLCCGKNP-LGDDEASTTVSKTETSQVAPA* >P1;mrg-tm sequence:mrg-tm: : : : ::: 0.00: 0.00 --------------------------------------- LS-LTVLTCIVSLVGLTGNAVVLWLLG ---------- FSIYILNLAAADFLFLSGRLIYSL- ---------------- ILYPVMMFSYFAG-LSFLSAV---- --------------------- HLSAVVCVLLWALSLLRS---IL ----------------------------- FITVAWLIFLCVVLCGSSLVLLI-- ------------------------- -YVTILLTVLVFLLCGLPF-GIQFF ----------------- LVSI--FLSALNSSANPIIYFFV ------------------------------------------------* thank you very much!

2 1

help--model-segment.py
by jinlian05＠lzu.cn 03 Jun '07

03 Jun '07

Hi: I want to use a part structure of template which belongs GPCR family. I write 'model-segment.py' scripts to model, the following is the scripts: from modeller import * log.verbose() class mymodel(automodel): def selection_atoms(self): self.pick_atoms(selection_segment=('37:A','63:A'), selection_search='segment',pick_atoms_set=1, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('74:A','96:A'), selection_search='segment',pick_atoms_set=2, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('111:A','133:A'), selection_search='segment',pick_atoms_set=3, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('153:A','173:A'), selection_search='segment',pick_atoms_set=4, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('203:A','224:A'), selection_search='segment',pick_atoms_set=5, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('250:A','274:A'), selection_search='segment',pick_atoms_set=6, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('287:A','308:A'), selection_search='segment',pick_atoms_set=7, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') env=environ() env.io.atom_files_directory='./:../atom_files' env.edat.nonbonded_sel_atoms=2 a=mymodel(env, alnfile='1u19-tm.ali', knows='1u19', sequence='mrg-tm') a.starting_model=1 a.ending_model=1 a.make() But when I run the mod9v1, there appears some errors: Traceback (most recent call last): File "model-segment.py", line 3, in ? class mymodel(automodel): NameError: name 'automodel' is not define How to define the 'automodel', please? thanks a lot!!

2 1

a question about add hidrogen
by Atila Iamarino 01 Jun '07

01 Jun '07

Hi there, I have this py file to include disulfide bonds: from modeller import * from modeller.automodel import * class mymodel(automodel): def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['85:B'],self.residues['111:B'])) log.verbose() env = environ() a = mymodel(env, alnfile = 'multiple.ali', knowns = ('1', '2'), sequence = '3', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1 a.ending_model = 10 a.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) I want to include hidrogens to the protein and a substrate that's on one of the templates to make a simulated annealing. And by the way, modeller does not make simmulated annealing wrigth? -- 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

2 1

Model with ligand from template
by hori koshii 31 May '07

31 May '07

Hello all, I have some doubt on modelling with ligand and need your help. I have go over the tutorial on ligand but still I am not able to create my own. I would like to include the ligand from the template pdb for the the models. In my case, the substrate is cellotetraose (4 glucose units). Should one or four dots (....) to be added at the end of the alignment? My other question in how do you build the alignment file (ali)? Do you simply add the dots to the alignment file or is there any tricks? (I am wondering do we need to modify the PDB file to include the BLK or HETATOM, and then create the ali?) When I tried to simply add the dots to the ali file and ran the script to build the model, I got error with the structures not being recognized and it complained about the sequence length. Please kindly give us some advice or share with me your own precious experience if you've already done the same thing. Thank you so much! Sincerely yours, Jas --------------------------------- Get the Yahoo! toolbar and be alerted to new email wherever you're surfing.

2 1