January 2015 - modeller_usage

Not refining the CAs of certain residues
by Edelmiro Moman 04 Feb '15

04 Feb '15

Hello, I would like to build protein models in which the CA coordinates of certain residues are identical to those of the (single) template. If I have understood it correctly, the following should do precisely that: class MyModel(automodel): def select_atoms(self): # Refine all atoms except the CAs of residues20-40 and 70-80 : return selection(self) - selection(self.residue_range('20', '40')).only_atom_types('CA') return selection(self) - selection(self.residue_range('70', '80')).only_atom_types('CA') Where the residue numbers correspond to those of the model. Is this correct? Or, if it makes more sense restricting the full backbone of the selected residues, would the following work? class MyModel(automodel): def select_atoms(self): # Refine all atoms except the backbone atoms of residue 20-40 and 70-80: return selection(self) - selection(self.residue_range('20', '40')).only_mainchain() return selection(self) - selection(self.residue_range('70', '80')).only_mainchain() Best regards, Miro -- Edelmiro Moman, PhD ProSciens, computer-aided drug design 2-4 rue du Palais de Justice L-1841 Luxembourg Phone : +352 2728-2588 E-mail : moman(a)prosciens.com http://prosciens.com

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Fwd: Request for you Assistance - Molecular modeling
by Swetha Kumari 12 Jan '15

12 Jan '15

---------- Forwarded message ---------- From: Swetha Kumari <swethakumari.k(a)gmail.com> Date: 12 January 2015 at 14:10 Subject: Request for you Assistance - Molecular modeling To: modeller-care(a)salilab.org Dear Sir, I have requested for Modeller 9.13 software, got License and installed ti successfully. I am following the script files and commands as per the manual exactly. But, unable to run some script files in the process of modelling. I have troubleshooted a lot and finally mailing you for your assistance. I want to do modeling using Modeller software. It gives the best possible models. I request you to kindly help me in sending modeling procedure little more in detail. I need ".py" file creation steps too. I will be highly thankful, if am done with modelling using modeller.. Awaiting your reply Thanking you, Yours faithfully, Swetha kumari K.

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using Modeller for building models using contacts and secondary structures
by Adhikari, Badri (MU-Student) 06 Jan '15

06 Jan '15

Hello, I used Modeller to reconstruct around a 100 proteins with true residue-residue contacts and secondary structure information. I could reconstruct only a few proteins with high accuracy. Below is a sample script I used for Modelling. I did not use any templates. (I found that Modeller satisfies more contact restraints when I provided a template with just one residue's coordinates instead of an extended structure as a template.) I wonder why Modeller could not satisfy true contact restraints. Is there any specific way to reconstruct proteins using true residue contacts? My PY files and PIR files look like this: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['.'] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Helices and Strands rsr.add(secondary_structure.strand(self.residue_range('3:', '11:'))) rsr.add(secondary_structure.strand(self.residue_range('16:', '26:'))) rsr.add(secondary_structure.alpha(self.residue_range('126:', '140:'))) # Contacts: rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CA:9'], at['CA:18']),mean=8.0, stdev=0.1)) rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:3'], at['CB:24']),mean=8.0, stdev=0.1)) rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:5'], at['CB:22']),mean=8.0, stdev=0.1)) rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:122'], at['CB:132']),mean=8.0, stdev=0.1)) a = MyModel(env, alnfile = '1f21.pir', # alignment filename knowns = 'empty', # codes of the templates sequence = '1f21') # code of the target a.starting_model= 1 a.ending_model = 20 a.make() C; >P1;empty structureX:empty: 1: : 152: : : :1.0: K-------------------------------------------------------------------------------------------------------------------------------------------------------* C; >P1;1f21 : : : : : : : : : KQVEIFTDGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGYQVE* Badri Adhikari University of Missouri ?

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