- modeller_usage - salilab.org

Query about symmetry in a multi-chain model
by Iván Felsztyna 25 Jul '18

25 Jul '18

Hi, I'm modelling a homopentamer using two templates. I want the five subunits of my model to be as much symmetrical as possible. So, I'm using the symmetry constrains that I found in the manual. The example script was built for a homodimer, so I adapted it to my homopentamer. I also included the indications to rename the chains and renumber the residues. However, the models I obtain show important structural differences between the different chains. I can see those differences visually and also when I plot the DOPE profiles of the five chains. I want to know if there is any mistake in my script, or something that I could add to it, in order to improving my results. Thank you in advance fot you help, Iván Felsztyna # Comparative modeling by the automodel class # # Demonstrates how to build multi-chain models # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') s5 = selection(self.chains['E']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) self.restraints.symmetry.append(symmetry(s1, s3, 1.0)) self.restraints.symmetry.append(symmetry(s1, s4, 1.0)) self.restraints.symmetry.append(symmetry(s1, s5, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) class MyModel(automodel): def special_patches(self, aln): # Rename both chains and renumber the residues in each self.rename_segments(segment_ids=['A', 'B', 'C', 'D', 'E'], renumber_residues=[1, 1, 1, 1, 1]) env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile='ali.ali', knowns=('a','b'), sequence=('r'), assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1 # index of the first model a.ending_model = 100 # index of the last model # (determines how many models to calculate) a.make() # do comparative modeling

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DOPE energy plot
by Mohammad Goodarzi 24 Jul '18

24 Jul '18

Hello, I have used the standard analysis to perform homology modeling. I have two questions now 1- I want to plot the DOPE energy plot between the template and the model but after running the evaluate_model.py , I only have one TvLDH.profile. So how can I get the other profile to be able to plot this figure? 2- what other plot I can make from the outputs ? I appreciate if one can refer me to a paper or something Thanks Mohammad

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homology modeling
by Mohammad Goodarzi 24 Jul '18

24 Jul '18

Hello, I have a WT protein which I got the structure from the PDB. I have a mutation happing on a single point amino acid. I want to see how this mutation influence on specific domian. I want to know if I am doing it right or not 1- I installed modeller on a Mac (high Sierra) 2- I search for the sequence on Uniprot and then I arange it as >P1;myseq sequence:myseq:::::::0.00: 0.00 with a * at the end of sequence and save it as myfile.ali what step should I follow and or which script should I use ? Thanks, Mohammad

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Query about structural alignment of a homopentamer with salign
by Iván Felsztyna 05 Jul '18

05 Jul '18

Hi, I'm trying to use the script salign_multiple_struc.py to obtain the structural alignment of two homopentamers. I want to use them as templates for a multi-template modelling. The problem is that the fitted pdb files that I obtain include only one of the subunits of each of the homopentamers, while I need the whole protein to be aligned. I copy here the script: log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files'] aln = alignment(env) for (code, chain) in (('4cof_extracelular', 'A'), ('4cof_extracelular', 'B'), ('4cof_extracelular', 'C'), ('4cof_extracelular', 'D'), ('4cof_extracelular', 'E'), ('glucl', 'A'), ('glucl', 'B'), ('glucl', 'C'), ('glucl', 'D'), ('glucl', 'E')): mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=code+chain) for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True), ((1., 0.5, 1., 1., 1., 0.), False, True), ((1., 1., 1., 1., 1., 0.), True, False)): aln.salign(rms_cutoff=3.5, normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree', alignment_type='tree', # If 'progresive', the tree is not # computed and all structues will be # aligned sequentially to the first #ext_tree_file='1is3A_exmat.mtx', # Tree building can be avoided # if the tree is input feature_weights=weights, # For a multiple sequence alignment only # the first feature needs to be non-zero improve_alignment=True, fit=True, write_fit=write_fit, write_whole_pdb=whole, output='ALIGNMENT QUALITY') aln.write(file='1is3A.pap', alignment_format='PAP') aln.write(file='1is3A.ali', alignment_format='PIR') # The number of equivalent positions at different RMS_CUTOFF values can be # computed by changing the RMS value and keeping all feature weights = 0 aln.salign(rms_cutoff=1.0, normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree', alignment_type='progressive', feature_weights=[0]*6, improve_alignment=False, fit=False, write_fit=True, write_whole_pdb=False, output='QUALITY'). Thank you in advance for your help, Ivan Felsztyna

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Query Regarding Running Modeller From Mac
by Aparna Bahuguna 02 Jul '18

02 Jul '18

I installed modeller on Macbook Pro OS X Yosemite 10.10.5. But it does not work. I made the python files and transferred them to the bin folder in library. Then I opened terminal and gave the command: *python model-default.py > model-default.log* but it said permission denied. I installed python separately still it did not work. Kindly suggest how can I run modeller through Mac Book. -- Aparna Bahuguna c/o Prof. D. S. Rawat Department of Chemistry University of Delhi New Delhi - 110007

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Re: [modeller_usage] Query Regarding Running Modeller From Mac
by Ajasja Ljubetič 02 Jul '18

02 Jul '18

Yes, you do not need that file. Just call python file-i-have-prepaired.py Try to run the examples first. On Mon, 2 Jul 2018 at 10:31, Aparna Bahuguna <aparna.bahuguna04(a)gmail.com> wrote: > I have prepared the files. But I dont know how to prepare a > model-default.py script file. Even the example folder I downloaded did not > contain any such file. > > On Mon, Jul 2, 2018 at 1:57 PM, Ajasja Ljubetič <ajasja.ljubetic(a)gmail.com > > wrote: > >> Hi! >> >> Probably you should first go through the tutorials: >> https://salilab.org/modeller/tutorial/ >> >> Which will show you how to prepare files etc. >> >> Best, >> Ajasja >> >> On Mon, 2 Jul 2018 at 10:25, Aparna Bahuguna <aparna.bahuguna04(a)gmail.com> >> wrote: >> >>> Whenever I type the command model-default.py it says no such file or >>> directory found. How should I prepare this file. Even when I downloaded the >>> example files there was no such file found. >>> >>> On Sun, Jul 1, 2018 at 11:48 PM, Aparna Bahuguna < >>> aparna.bahuguna04(a)gmail.com> wrote: >>> >>>> I installed modeller on Macbook Pro OS X Yosemite 10.10.5. But it does >>>> not work. I made the python files and transferred them to the bin folder in >>>> library. Then I opened terminal and gave the command: *python >>>> model-default.py > model-default.log* but it said permission denied. I >>>> installed python separately still it did not work. Kindly suggest how can I >>>> run modeller through Mac Book. >>>> >>>> -- >>>> Aparna Bahuguna >>>> c/o Prof. D. S. Rawat >>>> Department of Chemistry >>>> University of Delhi >>>> New Delhi - 110007 >>>> >>> >>> >>> >>> -- >>> Aparna Bahuguna >>> c/o Prof. D. S. Rawat >>> Department of Chemistry >>> University of Delhi >>> New Delhi - 110007 >>> _______________________________________________ >>> modeller_usage mailing list >>> modeller_usage(a)salilab.org >>> https://salilab.org/mailman/listinfo/modeller_usage >>> >> > > > -- > Aparna Bahuguna > c/o Prof. D. S. Rawat > Department of Chemistry > University of Delhi > New Delhi - 110007 >

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Reg. Evaluation of multiple template based multi models in one script
by KEDAR SHARMA 14 Jun '18

14 Jun '18

Dear all, i have generated 50 models of my protein using advanced modeling, now i want to evaluate all the models using one script which will give DOPE score, GA341 and molpdf score. Thank you very much. -- -- with regards KEDAR SHARMA PhD Scholar, BSBE Indian Institute of Technology, Guwahati

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Imposing rigid body restraint
by Richard E. Gillilan 05 Jun '18

05 Jun '18

Trying to hold a range of atoms rigid during optimization. I get an error message. Can anyone spot what I’m doing wrong here? Code: class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(secondary_structure.alpha(self.residue_range('138:A','149:A'))) rsr.add(secondary_structure.alpha(self.residue_range('523:B','530:B'))) r1 = rigid_body(self.residue_range('152:A','384:A')) rsr.rigid_bodies.append(rigid_body(r1)) a = MyModel(env, alnfile='KdpD_full_align.ali', knowns=('KdpD_GAF_bent_dimerA','KdpD_GAF_bent_dimerB','4CTI_mod_HAMP-delA','4CTI_mod_HAMP-delB'), sequence='KdpD_GDK_homodimer', assess_methods=(assess.DOPE, # #soap_protein_od.Scorer(), assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() ———— Result: Traceback (most recent call last): File "model-single-restraint.py", line 28, in <module> a.make() File "/Library/modeller-9.19/modlib/modeller/automodel/automodel.py", line 112, in make self.homcsr(exit_stage) File "/Library/modeller-9.19/modlib/modeller/automodel/automodel.py", line 561, in homcsr self.mkhomcsr(selection(self), aln) File "/Library/modeller-9.19/modlib/modeller/automodel/automodel.py", line 649, in mkhomcsr self.special_restraints(aln) File "model-single-restraint.py", line 15, in special_restraints rsr.rigid_bodies.append(rigid_body(r1)) File "/Library/modeller-9.19/modlib/modeller/util/modlist.py", line 77, in append self[dim] = obj File "/Library/modeller-9.19/modlib/modeller/util/modlist.py", line 38, in __setitem__ self._setfunc(ret, val) File "/Library/modeller-9.19/modlib/modeller/rigid_body_list.py", line 24, in _setfunc _modeller.mod_rigid_body_set(mdl.modpt, indx, obj._get_base_atoms(mdl), File "/Library/modeller-9.19/modlib/modeller/rigid_body.py", line 18, in _get_base_atoms return mdl.get_list_atom_indices(self._atoms, None) File "/Library/modeller-9.19/modlib/modeller/coordinates.py", line 298, in get_list_atom_indices (objinds, mdl) = obj.get_atom_indices() AttributeError: 'rigid_body' object has no attribute 'get_atom_indices'

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Modeller 9.20 release
by Modeller Caretaker 05 Jun '18

05 Jun '18

A new version of Modeller, 9.20, 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 9.20 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.20 is primarily a bugfix release relative to the last public release (9.19). See the Modeller manual for a full change log: https://salilab.org/modeller/9.20/manual/node40.html If you encounter bugs in Modeller 9.20, please see https://salilab.org/modeller/9.20/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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mutation including fixed new-atom/old-atom distance
by Maria Sola i Vilarrubias 29 May '18

29 May '18

Dear modeller supporters, I want to generate a single site mutation in a dimer and for this, I have successfully run mutate_model.py. However, in the new model, I would like to impose a fixed distance between a nitrogen from the mutated residue and an oxygen from a second residue that belongs to the other subunit. In detail: I want to mutate residue 38 from molA to Arg, and impose that the NE from new Arg38 is at a 2.68 Angstroms distance of molB Glu27 OE1. To impose this I understand I should write: rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['OE1:27:B'], at['NE:38:A']), mean=2.68, stdev=0.1)) But I don't know where to add this in mutate_model.py Could you please help me with this? With best regards, Maria -- Maria Solà Dep. Structural Biology IBMB-CSIC Barcelona Science Park (Helix Building) Baldiri Reixac 15 08028 BARCELONA Spain Tel: (+34) 93 403 4950 Fax: (+34) 93 403 4979 e-mail: maria.sola(a)ibmb.csic.es

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