July 2019 - modeller_usage

Libs not read correctly
by Danilo Boskovic 25 Jul '19

25 Jul '19

Dear all, when i attempt to run modeller through chimera interface (local) it works, but when i attempt to run my own script i get: Traceback (most recent call last): File "modeller.py", line 1, in <module> from modeller import * File "/home/harald/Desktop/Projectfiles/Repo/Input files/5xwp/modeller.py", line 3, in <module> env = environ() NameError: name 'environ' is not defined The script i run is: from modeller import * env = environ() aln = alignment(env) mdl = model(env, file='5xwp_all_4', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='5xwpA', atom_files='5xwp_all_4.pdb') aln.append(file='sequence.ali', align_codes='sequence') aln.align2d() aln.write(file='TvLDH-1bdmA.ali', alignment_format='PIR') aln.write(file='TvLDH-1bdmA.pap', alignment_format='PAP') My installation was successful but something is wrong.

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Problem modeling B-sheet
by oivalf_nix＠yahoo.com 22 Jul '19

22 Jul '19

Hi. I am trying to model a protein that has a C-terminal region without template match. However, the secondary structure prediction strongly suggests that part of this terminal region forms a beta-strand (residues 125 to 128). I am trying to generate an antiparallel beta sheet from this terminal segment, bonding with a pre-existing beta strand (residues 79-82). However, the generated model does not answer this command, being equal to the model generated without the command. Could you point out what I am doing wrong? Below are the script file. Thanks in advance. # Homology modeling with multiple templates 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 env.io.water = True # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class MyModel(automodel): def special_patches(self, aln): rsr = self.restraints at = self.atoms # A disulfide between residues: self.patch(residue_type='DISU', residues=(self.residues['9'], self.residues['30'])) self.patch(residue_type='DISU', residues=(self.residues['53'], self.residues['74'])) # Two beta-strands: rsr.add(secondary_structure.strand(self.residue_range('79:', '82:'))) rsr.add(secondary_structure.strand(self.residue_range('125:', '128:'))) # An anti-parallel sheet composed of the two strands: rsr.add(secondary_structure.sheet(at['N:79'], at['O:128'], sheet_h_bonds=-4)) a = MyModel(env, alnfile = 'Maycon3-1template.ali', knowns = '1template', sequence = 'Maycon3', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 100 a.make()

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How to skip automatic loop modeling?
by Yoochan Myung 22 Jul '19

22 Jul '19

Hello everyone, As mentioned in the title, is there any way to ignore/skip loop modeling in MODELLER9v21? My script is as follows: ==========[script]============ env = environ() a = automodel(env, alnfile='HM_1KTZ-202_het.ali', knowns='202_het', sequence='TGFbeta1_HM_1KTZ', assess_methods=(assess.DOPE, #soap_protein_od.Scorer(), assess.GA341)) a.starting_model = 1 a.ending_model = 3 a.make() ==========[script]============ My template has a missing loop (13 amino acids long) but MODELLER automatically links before/after the loop region for the modeled structures, which looked quite unreasonable. Many thanks, YooChan -- —————— Yoochan Myung *PhD student | Ascher Lab* Department of Biochemistry and Molecular Biology The University of Melbourne 30 Flemington Road, Parkville VIC 3010, Australia m: 0421188971 | e: ymyung(a)student.unimelb.edu.au

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Modeller homology modelling loops
by Danilo Boskovic 22 Jul '19

22 Jul '19

Dear all, I have two molecules in two different conformations due to two different ligands (CRISPR crRNA/crRNA+target RNA). When i compare the structures where the loops are missing the RMSD are 1.4 and 2.0 (20-30 total non-loop residues aligned). Would you use homology modeling or de novo? I think considering the RMSD that one might be able to model it using the missing residues as a template and homology model the target structure with loop refinement but this is my first attempt at doing homology modeling hence i am very reluctant to take any of my deductions as 100% viable solutions. Thanks, D. B.

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Loop modelling adjacent residue movement
by Danilo Boskovic 22 Jul '19

22 Jul '19

Dear all, What do you suggest for adjacent residue movement for modeling (xray) missing flexible loop structures? Do i assume the author has already removed all residues that are supposed to be modeled or do i assume that the end-point residues of the loops are to be modeled as well? Thanks D.B.

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