- modeller_usage - salilab.org

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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Homology modeling with low sequence identity and missing loops in template
by Ahmad Khalifa 05 Sep '19

05 Sep '19

Hello, I have two sequences with low sequence identity and I get an alignment in modeller different than clustalW, which also differs from when I use emboss matcher. I also have a missing segment in my template, I want the final model to have the corresponding segments and the gaps unmodeled, same as the template. I tried to modify the alignment manually, however I ran into the "SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb :" error, which I think has to do with the number of residues in the header of the alignment. I attached the modeller and matcher alignments, in pir and fasta respectively. I would appreciate if you tell me how to prevent the missing loops in the template from being built and how to modify the alignment manually bypassing the above error. Also, do give your input regarding the difference in alignments, and how to choose the most accurate one. I'm also fine with sharing the files privately. Best regards.

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Modeling missing residues from a second template file
by Danilo Boskovic 20 Aug '19

20 Aug '19

Dear Ben, Is it possible? I know that i can model residues according to the tutorial: select the residues and use as a template to model the full structure. So i did it and the structure was severely impacted (RMSD 0.25). Loopmodel de-novo can do it without problems although i wish i could utilize my other structure file that is basically just a different conformation due to a ligand, but the deviation at the positions where the residues are missing are minuscule. If not then i have two choices: de-novo and the automodel with a change in conformation of 0.25 RMSD. Which one would you choose? Sincerely, D. Boskovic

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loop modeling
by Rui Chen 20 Aug '19

20 Aug '19

Hello, I am using Chimera (Modeller) to model a loop, which locates at the C-termini of the original crystal structure. The structure of the target protein is a homodimer, however, I cannot model the two chains together. How can I model the two chains together? I modeled chain A and chain B separately, the loops I modeled have different configurations. Could you please help me resolve the problem? Best regards, Rui

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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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