December 2009 - modeller_usage

Modeling ligands in the binding site
by Qinghua Liao 10 Dec '09

10 Dec '09

Hi modeller users, Can modeller do ligand-steered modelling? And what is the difference between the ligand-steered method and the mothods from the on-line tutorial of Modeling ligands in the binding site? Are they the same method? Thanks very much! All the best, Qinghua fantasticqhl(a)yahoo.com

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Modeller on PPC64 with Linux - installation
by Wojciech Stach 09 Dec '09

09 Dec '09

Hello, Is there any way I could get Modeller installed on my machine: PPC64 with running Linux SLES 11? I browsed through all the downloadable files and it seems like none of them would be suitable to the abovementioned configuration... Any help will be greatly appreciated! Thanks, Wojciech

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Virtual conference Inbix '10: Cfp/Registrations starts!!
by Prash 08 Dec '09

08 Dec '09

Dear All, The first Indian virtual conference on Bioinformatics 2010 (Inbix'10): http://www.bioinformatics.org/wiki/Inbix10 Excellent opportunity to interact with leading scientists in the world in the area of Bioinformatics and Systems Biology! All for just Rs 500/- or 10 USD All the best Prash Prashanth Suravajhala C-DAC-Bioinformatics Group, Pune, India http://wiki.bioinformatics.org/prash I 'put a fullstop' as soon as I see myself complaining and blaming. These two habits destroy my inner power completely, because they show I am still expecting solutions and changes from others. Courtesy: Thought for Today

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Fw: Re: update
by leuven 06 Dec '09

06 Dec '09

I have made a new script and figured it out, the caculation speed is very fast now, thanks!

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update
by leuven 06 Dec '09

06 Dec '09

Dear all, I found the solution to include disulfide bonds, while the later problem is how to combine multiple cpu caculation and including disulfide bridges together? they can be performed indenpendently but not together, could you please give me some suggestion? model.py # Example of changing the default optmization schedule from modeller import * from modeller.automodel import * from modeller.parallel import * j = job(modeller_path="/usr/lib/modeller9v7/bin/modslave.py") j.append(local_slave()) # 1 Processor j.append(local_slave()) # 2 Processors j.append(local_slave()) # 3 Processors j.append(local_slave()) # 4 Processors class Mymodel(automodel): def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['151'],self.residues['181'])) self.patch(residue_type='DISU', residues=(self.residues['422'],self.residues['448'])) self.patch(residue_type='DISU', residues=(self.residues['420'],self.residues['482'])) log.verbose() env = environ() # Give less weight to all soft-sphere restraints: env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7) env.io.atom_files_directory = ['.', '../atom_files'] a = Mymodel(env, alnfile='GBSS1-mult.ali',knowns=('2r4tA','3copA','3cx4A'), sequence='GBSS1') a.starting_model =1 a.ending_model = 60 # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 8 a.max_molpdf = 1e8 a.use_parallel_job(j) a.make() error: 'module' object has no attribute 'Mymodel' from <Slave on localhost>

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disulfide building problem
by leuven 06 Dec '09

06 Dec '09

Dear All, I want to build a model including 3 disulfide bridges, but my script could not build bridges while modelling. Can you give me some suggestion on how to make the bridges-making script work? from modeller import * from modeller.automodel import * log.verbose() env = environ() env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7) env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, alnfile='GBSS1-mult.ali',knowns=('2r4tA','3copA','3cx4A'), sequence='GBSS1') class automodel: def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['151'],self.residues['181'])) self.patch(residue_type='DISU', residues=(self.residues['422'],self.residues['448'])) self.patch(residue_type='DISU', residues=(self.residues['420'],self.residues['482'])) a.starting_model =1 a.ending_model = 60 a.library_schedule = autosched.slow a.max_var_iterations = 300 a.md_level = refine.very_slow a.repeat_optimization = 8 a.max_molpdf = 1e8 a.use_parallel_job(j) a.make()

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