- modeller_usage - salilab.org

How to optimize a model
by Atila Iamarino 06 Jul '07

06 Jul '07

Dear Ben Webb, Thanks for everything you have been very helpful. I'm trying to include one model I generated in the optimization scrip fro FAQ: from modeller import * from modeller.automodel import * log.verbose() env = environ() a = automodel(env, alnfile='align1.ali', knowns='templ1', sequence='targ1') # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Very thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 3 a.max_molpdf = 1e6 a.make() How can I do it? And how can I automate it including on this script to optimize only the best model: from modeller import * from modeller.automodel import * log.verbose() env = environ() a = automodel(env, alnfile = '1', knowns = ('2', '3'), sequence = 'bar', 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]) a.make() Thanks again, -- 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

pdb95.fsa
by Bo Yang 06 Jul '07

06 Jul '07

Hello, Modeller: I try to do a search for potentially related sequences of known structure by using the "build_profile.py" from the "command" section of Modeller9v1. But the program complaines that "Cannot open file pdb95.fsa: no such files". I search the Modeller9v1 package, and can't find the file named as "pdb95.fsa". Do you know where can I find the "pdb95.fsa" file? Or is there an alternative file that can be used as the "pdb95.fsa" in the program package? I notice that there is a file called "pdball.pir" from the download section of Modeller. Is this one can be used as a database? If so, how can I change the file format to .fsa? Thank you. I use modeller9v1. Bo --------------------------------- Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.

2 1

same values for the models 2
by Atila Iamarino 03 Jul '07

03 Jul '07

Dear Ben Webb, Do you have any example (.py file) of these changes, I can't find any on the examples that came with Modeller. Thanks! -- 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

How to bend a helix?
by "Nadine Töpfer" 03 Jul '07

03 Jul '07

Hi all! I am facing a problem concerning a ringlike alpha-helical structure. My initial crystal-structure has a diameter of 9nm which I want to shrik down to about 7nm, without destroying the helix. Does anybody know how to solve this problem using modeller? thanks -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS. Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail

2 1

ternary complex in modweb
by James Fethiere 03 Jul '07

03 Jul '07

Hi, I'm trying to generate a model of an interleukine receptor complex using modweb. I have modelled separately 2 of the partners using modweb, and superimposed the models on the the template in pymol. However, modweb cannot find a reliable template of the last partner (which corresponds to a 4 hlx IL). I guess I can use the full ternary complex as a template, but don't see how this can be done within modweb. Any idea? Thanks James

2 1

Same values for the models
by Atila Iamarino 03 Jul '07

03 Jul '07

Hi all, Is there a reason for different runs of the same .py file give exactly the same model, with the same DOPE score and all? Does Modeller make aways the same pathway? thanks very much, -- 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

Help with transfer_xyz method
by Ali Algarrous 02 Jul '07

02 Jul '07

Hello, I have a sequence and a structure aligned in a file in RIP format. Now I want to just copy the coordinates of our structure to our sequence without any changes. I am using transfer-xyz.py but it doesn't copy the coordinates as they are in the structure before or after the loops. Is there a way to transfer the coordinates from structure to sequence as they are? Regards, Ali Algarrous

2 3

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

2 1

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

2 1

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()

2 1