- modeller_usage - salilab.org

Charmm error : missing residues
by Yogesh Sharma 18 Feb '20

18 Feb '20

Hi everyone I used modeller to generate structure of my membrane protein. But when I am using that structure in charmm gui to build setup. I am getting error stating missing residues or error in pdb. How can I rectify it? -- * with regards* *Yogesh Sharma*

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Modeller will only read the first 4096 characters of this line.
by Yogesh Sharma 18 Feb '20

18 Feb '20

Hi iam new to modeller. readlinef__W> File: pdb_95.pir, Line: 421 Modeller will only read the first 4096 characters of this line. readlinef__W> File: pdb_95.pir, Line: 29819 Modeller will only read the first 4096 characters of this line. readlinef__W> File: pdb_95.pir, Line: 29829 Modeller will only read the first 4096 characters of this line. readlinef__W> File: pdb_95.pir, Line: 29839 Modeller will only read the first 4096 characters of this line. readlinef__W> File: pdb_95.pir, Line: 29846 Modeller will only read the first 4096 characters of this line. readlinef__W> File: pdb_95.pir, Line: 29852 No more warnings will be printed for truncated lines in this file. Are these warnings safe?

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how to generate the ini file only
by Li Xue 06 Feb '20

06 Feb '20

Hello all, Does anyone know how to ask modeller to generate the ini file and stop? I tried the following but failed: a = automodel(env, alnfile='my_alignment.ali', > knowns='3mrb', sequence='query', > assess_methods=assess.DOPE) > aln = alignment(env) > aln.append(file='T3mrb_Q1duz.ali') > a.transfer_xyz(aln) Best, Li

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Molecules MEX and CME
by Daniel Evans 03 Feb '20

03 Feb '20

Hi all- The MODELLER documentation at https://salilab.org/modeller/manual/node149.html#MEMB:iodata.convertmodres says the following: "Some special handling is done for certain commonly-used modified residues. The MSE residue type is mapped to the regular MET amino acid, and the SE atom in this residue is mapped to SD. The MEX and ABU residue types are both mapped to CYS." According to https://salilab.org/archives/modeller_usage/2003/msg00051.html the reason for this is that MEX is "cysteine bridged with beta-mercaptoethanol". I recently encountered PDB ID 3OW6. This structure includes a ligand labeled MEX. The ligand does not resemble CYS, and the presence of MEX causes an error. I'm reluctant to set io_data.convert_modres to False, because I'd like to handle other modified residues (ex. MSE). I was able to work around the issue, so it didn't impact me too much. But I thought I should say something in case others run into the same issue. I see that the ligand CME does resemble CYS, with beta-mercaptoethanol attached through a disulfide bond. Is it possible that MEX and CME are switched? Best, Daniel Evans

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Use modeller with slurm
by Mariana GONZALEZ MEDINA 10 Jan '20

10 Jan '20

Hello, I would like to know if there is a way in which I can use parallel jobs to create 1,000 models with slurm, since I can't use the sge_qsub_job command. Thank you. Mariana

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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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