- modeller_usage - salilab.org

Alignment problem
by Monika Sharma 30 Jun '07

30 Jun '07

Dear All, I am trying to do modelling of a protein, for whom i got the hits for psi-blast. Now, BLAST showed that the first ~100 residues to be in homology with one set of proteins, and the rest with other set of proteins. So for having the desired result, i broke the protein in two parts, one part of first ~100 residues with two or more proteins showed by BLAST search, and then the other part with its respectives subjects. So now i have two modelled parts of protein, but dont know how to link them, and important thing is that end of the former is the beginning of the other. My questions are: 1. Is it the right way of doing? 2. If yes, can somebody suggest me how to link these parts? 3. An alternative way seems to be like alignment of chimeric protein, but i am not able to get the desired results in first step of alignment of the multiple templates. Can there be any way to give your own alignment files as .ali and .pap? Because when i am trying to give manually in the usual manner, then the program is looking for the _fit.pdbs files formed at the first step, and complaining of no match... I have really got stuck at the end.... :-( if anybody can please help me out........... Thanks in advance... Monika

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Loop Modelling
by Michael Paterson 30 Jun '07

30 Jun '07

Good morning I have been generating models using the dopehr_loopmodel route, having decided it would be more efficient to only generate loop models for the lowest energy comparative model I switched to generating structures using the automodel class and then defining the loop regions by visualizing the lowest energy structure and plugging the values in to the 'Loop refinement of an existing model' example script provided with Modeller 9v1. The resulting loop models do not generate models of nearly the same quality - as judged by Ramachandran plots - than the automatically generated loop models. Is there a convenient way to extract the loop sequence information that loop model uses to generate it's models. Regards Mike Paterson

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set alpha-helix and SS bond
by Aline 30 Jun '07

30 Jun '07

Hi list, Im trying to model a 5 chains protein, wich 3 of them are long alpha-helix. Well, I would like to set some residues as part of these helixes, and a SS bridge. When I try to tell modeller 9v1 to do that (with the enclose script), I keep receiving the following error: ---------------------------------------------------------------------------- C:\teste2>mod9v1 model_ss_alpha.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "model_ss_alpha.py", line 31, in ? a.make() File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel .py", line 108, in make self.homcsr(exit_stage) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel .py", line 419, in homcsr self.make_initial_model(aln) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel .py", line 433, in make_initial_model self.generate_method(self, aln) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\generate. py", line 25, in transfer_xyz mdl.create_topology(aln) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\automodel\automodel .py", line 605, in create_topology self.special_patches(aln) File "model_ss_alpha.py", line 18, in special_patches self.patch(residue_type='DISU', residues=(self.residues['1070'], File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\coordinates.py", li ne 165, in __getitem__ (self.offset, self.length, self.suffix)) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\util\modutil.py", l ine 76, in handle_seq_indx int_indx = lookup_func(*args) File "C:\Arquivos de programas\Modeller9v1\modlib\modeller\coordinates.py", li ne 50, in _indxres raise KeyError, ("No such residue: %s" % indx) KeyError: 'No such residue: 1070' -------------------------------------------------------------------------- What might be wrong? Thanks, Aline ------------------------------------------------------------------- This is the script: from modeller import * # Load standard Modeller classes from modeller.automodel import * # Redefine the special_restraints routine to include the secondary # structure restraints (this routine is empty by default): class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints # An alpha-helix: rsr.make(aln, restraint_type='ALPHA', residue_ids= ('1118:', '1131:'), spline_on_site=False) # 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['1070'], self.residues['1122'])) # This is as usual: log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' env.io.hetatm = env.io.water = True a = mymodel(env, alnfile='a6b1lam.ali', knowns=('a6b1lam_model_0.3'), sequence='a6b1_lam') a.starting_model = 1 a.ending_model = 1 a.make()

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h-bonds with loop models
by David Gell 30 Jun '07

30 Jun '07

Dear modellers i am trying to build models for a single missing loop on a known xtal structure and i have a couple of questions 1) can modeller introduce hydrogen bonds in loop modelling (is it true that all-hydrogen models are not fully implemented for loop modelling)? 2) is it true that modeller does not include hydrophobic packing factors? i currently have models with fully exposed hydrophobics that have similar 'modeller objective function' to those with more buried hydrophobic sidechains. i'm a modeller newbie, and above is based on my understanding (i.e. likely flawed) of the mail archives and docs. perhaps i should be introducing some 'artificial' distance restraints to mimic the effects of the above interactions? any advice greatly received. cheers dave gell

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setting restyp, top_heav and par libs
by David Marshall 30 Jun '07

30 Jun '07

Dear Modellers, I am currently trying to model the effect of phosphorylation on a protein. I have been kindly provided with adapted top_heav.lib and par.lib files and I have modified restyp.lib accordingly. I have searched the manual but cannot find commands to set these .lib files in my .py files. I want to avoid overwriting the existing files as I do not have access. Many thanks for your time, David Marshall

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what should PYTHONPATH and LD_LIBRARY_PATH be set to?
by David Mobley 27 Jun '07

27 Jun '07

Hi, Sorry to ask such an apparently naive question, but I haven't been able to find the answer on the mailing list, or in the documentation, or by experimenting myself... In a generic linux installation, when I'm not using an RPM, what do I need to set the PYTHONPATH and LD_LIBRARY_PATH to, in order to be able to use modeller in the typical python way (i.e. "import modeller" from within python)? The documentation indicates this is possible with modeller 9v1, if the above paths are set appropriately, but it doesn't indicate what "appropriately" means. Thanks! David

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modelling a chimera from structureM-type templates
by Cahya Prihatna 27 Jun '07

27 Jun '07

I want to model a chimera protein which consists of two individual proteins. The crystallography of these proteins have not been reported, I was only able to find the model for them. How can I build the chimera based on models as templates? Regards, Cahya Prihatna

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build_profile.py help
by Eeson Rajendra 27 Jun '07

27 Jun '07

Hi I have a sequence that I want to check against known structures and am trying to run "build_profile.py". I get an error: ************** 'import site' failed; use -v for traceback Traceback (most recent call last): File "build_profile.py", line 10, in ? chains_list='ALL', minmax_db_seq_len=(1, 40000), clean_sequences=True) File "C:\Program Files\Modeller9v1\modlib\modeller\sequence_db.py", line 48, i n read minmax_db_seq_len) IOError: openf______E> Cannot open file pdb95.fsa: No such file or directory ************* The pdb95.fsa file is located in my Modeller9v1\examples\commands folder. Should it be moved? Additionally, I have downloaded the pdb_95.cod.gz, pdb_40.cod.gz and pdball.pir.gz files. I have unzipped them but am not sure which directory to place them in (or the files that they replace). Do I need to change their file extensions? Is pdb_95.cod the pdb95.bin file referenced in the example build_profile.py script? Any help would be appreciated. Eeson

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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

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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

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