- modeller_usage - salilab.org

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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python script error
by Bruno Cramer 31 May '19

31 May '19

Hi, I need some help has follows. I am using the script file as in example of pg 9 0f the User Manual. The error is given bellow: bcramer@schrodinger:~/workdir-modeller9.1$ python runmodeller-test1.py File "runmodeller-test1.py", line 13 a = automodel(env, alnfile = ’alinha.pir’, knowns = ’4hpg’, sequence = ’bgl’) ^ SyntaxError: invalid syntax script is as follows -------------------------------------------- # -*- coding: utf-8 -*- from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['home/bcramer/workdir-modeller9.1'] env.io.hetatm = True env.io.water = True a = automodel(env, alnfile = ’alinha.pir’, knowns = ’4hpg’, sequence = ’bgl’) a.starting_model = 1 a.ending_model = 5 a.make() ------------------------------------------ OS-Ubuntu 18.4 64b Modeller v.9.21 -Python 2.7 Thank you Bruno

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Solvation and randomization in ALLOSMOD glycan modeling
by Chakraborty, Srirupa 21 May '19

21 May '19

I am trying to use allosmod package in MODELLER for ab initio modeling of glycans as described in the paper "All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins" (Structures 2013. DOI: 10.1016/j.str.2013.02.004). I have two questions regarding the glycan modeling method, about which I could not find any prior discussions in this forum. My questions are: (1) In the glycan modeling methods section of the paper, it is mentioned that "initial structures were generated by addition of glycan chains with ideal geometries derived from CHARMM, followed by a 1angstrom randomization of the full atomic coordinates". I am assuming this randomization is the same as the randomize_xyz function of MODELLER. However, since templates are not being provided by the user for the glycans, how are the sugar ring puckerings and dihedral angles correctly reproduced even after such large random deviations? (2) My understanding is, in MODELLER, the solvation information is taken implicitly from the template provided. However, since the glycans are modeled template-free, is there any explicit treatment of solvation, or is the optimization done in vacuum? Thanks, -Srirupa

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how to use multiple templates and applying restraints based on one structure.
by Bisignano, Paola 26 Apr '19

26 Apr '19

Hi, I would like to model missing portion of a solved protein structure by using two different templates. I know that is pretty straightforward to use multiple templates, but I would like to include restraints based on the first entry only. Basically I would like to keep the first solved structure as it is, and just move the residues lining the missing portions, while using the second structure as a 'flexible' template. How can I define that I want the restraints based only on the first template? I tried to build a chimera, but I have a bunch of clashes if I do that. Thanks, Paola Paola Bisignano, Ph.D. postdoctoral research associate Department of Pharmaceutical Chemistry Cardiovascular Research Institute University of California, San Francisco

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