May 2007 - modeller_usage

difficult modelling example
by James Fethiere 31 May '07

31 May '07

Hi, I'm trying to reproduce the example for difficult modelling using the genThreader for alignment. This part works fine, and I get a model with ~28% id. Now, how do I get the alignment file from genthreader ready for modeller. There is a nice example but it does not say how one gets from html to the .ali file. Thank you James

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to build a structure from CA coordinate
by Lixia Jin 31 May '07

31 May '07

I ave a pdb file with only CA coodinate. In order to get a complete strutur I used MDELLER to builld a model. However, the CA atomes were shifted a bit in the model. How can I fix those CA atoms when I build a model? thanks!

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residue selection
by Lixia Jin 30 May '07

30 May '07

I have two chains in my model: A chain has 324 residues. I want to modify only part of chain A (193-249) and chain B. How do I select the residues? Thanks!

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define residues
by Lixia Jin 30 May '07

30 May '07

When I use: self.patch(residue_type='DISU', residues=(self.residues['199'], self.residues['205'])) it works. When I use: self.patch(residue_type='DISU', residues=(self.residues ['199:G'], self.residues ['205:G'])) it gives me error information: KeyError: 'No such residue: 199:G' What might be wrong? Thanks! ------ Atila Iamarino wrote: > I'm interested in modeling a protein forcing disulfide bridges but my > protein has two chains. How do I set the residue in the .py file? > > # 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['8'], > self.residues['45'])) That's straightforward - just include a chain ID (see http://salilab.org/modeller/9v1/manual/node153.html) For example, self.patch(residue_type='DISU', residues=(self.residues['8:A'], self.residues['45:A'])) Ben Webb, Modeller Caretaker

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ImportError: No module named automodel...
by matteo 30 May '07

30 May '07

hi! i've just installed modeller9v1 from the source code on a x386 pc... everything went fine, but as i run mod9v1 xxx.py, i get this message: Traceback (most recent call last): File "<string>", line 1, in ? File "/home/teo/_work/_m-i7/modeller.py", line 3, in ? from modeller.automodel import * # Load the automodel class ImportError: No module named automodel i'm just using the default script file, with the proper file name: # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:/home/teo/_work/_m-i7/' a = automodel(env, alnfile = 'm-i7.ali', # alignment filename knowns = '1f88', # codes of the templates sequence = 'm-i7') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling can anybody help me? many thanks matteo

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Including disulfide bonds
by Atila Iamarino 23 May '07

23 May '07

Hi all, I'm interested in modeling a protein forcing disulfide bridges but my protein has two chains. How do I set the residue in the .py file? # 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['8'], self.residues['45'])) -- 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

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disulfide
by Lixia Jin 17 May '07

17 May '07

Hi, First try MODELLER. It worked good. Then I added DISU as I learned from the manual by redefining the special_patches(). (Script as below) The new model is the same as the old one. I don't see disulfide bond between the two cysteins. Can any one explain it a bit? Thank you! Lixia ------------------ # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class #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 199-205 self.patch(residue_type='DISU', residues=(self.residues['199'], self.residues['205'])) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:..' a = mymodel(env, alnfile = 'align2.ali', # alignment filename knowns = 'e791', # codes of the templates sequence = 'spnG') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make () # do the actual homology modeling

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model transmenbrane regions
by jinlian05＠lzu.cn 16 May '07

16 May '07

Hi: My template protein belongs to the GPCR family,I want to only use the transmembrane regions of the template,and i want to get only TM regions of target protein, but i dont know how to do. When i align my model sequence using its TM region with my template protein ,also using template's TM region, i get not the TM structure, it look likes the whole structure, please?

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use bovin rhodopsin as template
by jinlian05＠lzu.cn 16 May '07

16 May '07

Hi: I want to use MODELLER9v1 to model the protein 3D structure, it belongs to the GPCR family, I choose bovin rhodopsin as the template. I want to only use the transmember regions of the template, but i dont know how to restraints the template sequence.Or is there another method i can use, please? Thanks a lot!

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Making many result model
by 서주현 16 May '07

16 May '07

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