December 2019 - modeller_usage

Modeller produces primary structure only
by Danilo Boskovic 03 Jan '20

03 Jan '20

Dear all, I tried to model part of my missing protein from a template but i fail to get proper structure (its just a linear line of amino acids) even though i followed the tutorial 100%. My script (it is properly spaced in my file): from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['.', './template_struc'] env.io.hetatm = True env.io.water = True class MyModel(automodel): def select_loop_atoms(self): return selection( self.residue_range('1154', '1298')) a = MyModel(env, alnfile = 'alignment.ali', knowns = '5xwp', sequence = 'sequence', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 1000 a.make() Alignment was proper and i checked every missing residue one by one. Dope scores are negative, GA scores 1.00). My templates are in /template_struc and this was tested to be working when i produced .ali files for my templates. So whats the problem? sincerely, D.B.

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Error - Unavailable server
by CYNTHIA CHRISTINA DE OLIVEIRA 26 Dec '19

26 Dec '19

Hello, I am trying to use the “Modeller (loops/refinement)” tool present in Chimera software and the following error message is displayed: NonChimeraError: Web service appears to be down. See Reply Log for more details. Service 'opal:Modeller9v8Service' is unavailable. See Reply Log for more details. Is this a temporary server issue or is there a problem with the version of the program I am using (Modeller9v8)? In the latter case, what should I do to resolve this situation? Thanks in advance, Cynthia de Oliveira

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Tweaking around with the same alignment
by Eugene Radchenko 19 Dec '19

19 Dec '19

Hello! Sometimes I want to play with different Modeller options and parameters while working with the same alignment file. However, to avoid overwriting the previous results, I actually have to modify the alignment file and Modeller script anyway by changing the target sequence name. Am I doing something wrong and is there a better way? Thank you in advance Eugene

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Nontrivial restraints
by Eugene Radchenko 19 Dec '19

19 Dec '19

Hello! I am trying to force a helical segment (that was built from the non-aligned part of the sequence) to be roughly between two other helical segments rather than sticking outside as automodel/loopmodel puts it by default. I have tried to create an angle restraint between the segment centroids but it seems to be ignored (apart from reporting its violation in the log). Is it possible to achieve in Modeller or should I actually specify restraints during further optimization/dynamics so that the segment rotates into desired place? Thank you in advance Eugene The simplified code snippet is like this (trying to achieve “linear” arrangement of A2, A3, and B2 centroids) def special_restraints(self, aln): rsr = self.restraints helixA2 = self.residue_range('42:A', '60:A') helixA3 = self.residue_range('65:A', '83:A') helixB2 = self.residue_range('42:B', '60:B') rsr.add(secondary_structure.alpha(helixA2)) rsr.add(secondary_structure.alpha(helixA3)) rsr.add(secondary_structure.alpha(helixB2)) helixA2c = pseudo_atom.gravity_center(selection(helixA2).only_atom_types('CA')) rsr.pseudo_atoms.append(helixA2c) helixA3c = pseudo_atom.gravity_center(selection(helixA3).only_atom_types('CA')) rsr.pseudo_atoms.append(helixA3c) helixB2c = pseudo_atom.gravity_center(selection(helixB2).only_atom_types('CA')) rsr.pseudo_atoms.append(helixB2c) rsr.add(forms.gaussian(group=physical.nmr_distance, feature=features.angle(helixA2c, helixA3c, helixB2c), mean=pi, stdev=0.1))

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Why Modeller gives me an error?
by Studia Studia 18 Dec '19

18 Dec '19

Hello. I need to optimize amino acids located 5A from the ligand for this purpose I use this code: #residues to optimize: select=selection(mdl1) select1=select.only_het_residues() select2=select1.select_sphere(5) select3=select2.only_std_residues() select4=select3.by_residue() mdl1.restraints.unpick_all() mdl1.restraints.pick(select4) select4.energy() select4.randomize_xyz(deviation=4.0) mdl1.env.edat.nonbonded_sel_atoms=2 optimize(select4, sched) mdl1.env.edat.nonbonded_sel_atoms=1 optimize(select4, sched) select4.energy() mdl1.write(file=model_name+'_docked_opt'+str(i)+'.pdb') This works for most structures but for a few I have this error: mdl.restraints.pick(select4) File "C:\Program Files (x86)\Modeller9.21\modlib\modeller\restraints.py", line 94, in pick raise ValueError("selection refers to a different model") ValueError: selection refers to a different model

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