- modeller_usage - salilab.org

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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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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Modeller 9.22 release
by Modeller Caretaker 21 Jun '19

21 Jun '19

A new version of Modeller, 9.22, 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 9.22 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.22 adds support for PDB hybrid-36 notation (to allow for more than 100,000 atoms in a model), adds chain IDs to neighbor and secondary structure output files, improves mmCIF support, and contains a number of bug fixes. See the Modeller manual for a full change log: https://salilab.org/modeller/9.22/manual/node40.html If you encounter bugs in Modeller 9.22, please see https://salilab.org/modeller/9.22/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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