- modeller_usage - salilab.org

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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selection.mutate then optimize Vs. homology modeling for point mutations
by Ammar, Ammar (Stud. SCI) 18 Nov '19

18 Nov '19

Dear all, I hope you can give me your opinion in my case. I have a 3D structure of a wildtype protein (X-Ray) and I want to mutate one amino acid (substitution) and obtain the new structure that contains the introduced structural changes by the mutation. Also, the sequence of the protein is known. I see an example on Modeller website for a Mutated model: https://salilab.org/modeller/wiki/Mutate%20model which show how to introduce a mutation and then the conformation of the mutant sidechain is optimized by conjugate gradient and refined using some MD. Another way of doing it is to provide the PDB file and an alignment of the protein sequence and its mutant version and perform homology modelling using Modeller. Any idea which method is preferable considering that both can be performed using Modeller to achieve the same goal here? Thank. Best regards.

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Modelling in/dels and residue substitutions
by Jared Slosberg 12 Nov '19

12 Nov '19

Hello, I am interested in creating models for variants of a protein with a known cryo-EM structure. My approach for the substitutions is to use the mutate_model script. However, I would also like to model predicted changes in structure to nearby residues. I altered the script in this way in an attempt to optimize over a range of residues, but I saw no difference in the resulting model than with only the one residue selected. modelname, respos, restyp, chain, start, stop, = sys.argv[1:] ... s = selection(mdl1.chains[chain].residues[start],mdl1.chains[chain].residues[stop]) Could you tell me if this change to the script would be expected to alter the resulting model, or if there is a better approach? As well, my approach to modelling deletions is to create a manual alignment in which the residues around the deletion are unaligned from the template, so that they fold freely, and choosing the model [ generated with model_single.py ] with the lowest DOPE score if inspection looks good. [Here, GFF deleted]. one segment of query: FNSSAFFFSVV---------FL aligned segment of template: FNSSA------FFFSGFFVVFL However, this has obviously left the ends of the aligned sections fixed in space, so that the region that I want to fold "freely" is fixed at these two points. This results in them "stretching out" rather than being able to fold as I would like. I hope that I am being clear. Is there better method to create variants with insertions that is more flexible? Thank you for your time, Jared

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Modeller 9.23 release
by Modeller Caretaker 29 Oct '19

29 Oct '19

A new version of Modeller, 9.23, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.23 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.23 adds support for Python 3.8 and improves handling of chain IDs, in particular allowing for multi-character chain IDs to be read from mmCIF files. See the Modeller manual for a full change log: https://salilab.org/modeller/9.23/manual/node40.html If you encounter bugs in Modeller 9.23, please see https://salilab.org/modeller/9.23/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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rwquest for licence key
by shah Faisal 11 Oct '19

11 Oct '19

plz give me key for use of modeller software

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Missing hetatms in model file
by Nirali Desai 10 Oct '19

10 Oct '19

Dear all, I have to model missing residues of the protein. PDB ID: 2hxh I also want to include het atoms (Ligands) in the resultant model. I did the required changes: 1. *env.io.hetatm = True * (Changed this in the model generation script) 2. .ali file >P1;kinesin structure:2hxh:1:A:1290:C:::: MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY/MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEGEEDEA/MASMTGGQQMGRDPINMPGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEKVSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKKTDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQIRNTVSVNLELTAEEWKKKHHHHHH/* Bcz, total residue count is 1290 and chains are A, B, C (chains are specified using the chain breaks). Is it correct please guide me on this. Will that read the hetatms too? Because when I run this and generate model. It didn't include the het atoms. Please help me on this. Sorry for the inconvenience. Thanking you, Nirali

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