- modeller_usage - salilab.org

Modelling with ligands while maintaining correct chain ID
by Ahmad Khalifa 17 Aug '18

17 Aug '18

Hello, I have a template that has the following structure: Chain A Chain B ligand 1 A ligand 2 A ligand 3 B ligand 4 B I edit my ali file to place 4 dots at the end of the second chain before the *. This results however, in having all four ligands as part of of the B chain in my model. How can I fix that? Regards.

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ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different
by Ahmad Khalifa 07 Aug '18

07 Aug '18

Hello, I'm trying to model a sequence of alpha beta tubulin based on template (3jar), with ligand included. After aligning the template and sequence according to this tutorial: https://salilab.org/modeller/tutorial/basic.html I'm doing the model building according to this: https://salilab.org/modeller/9.20/manual/node18.html After alignment, I edited my .ali file to look like this (adding the dots corresponding to the hetero atoms): >P1;3jar_template structureX:3jar_template.pdb: 1 :B:+861 :K:::-1.00:-1.00 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDS VRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTL LISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDL NHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPR---G--L-K-MSAT-F IGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQ--YQDAT./MRECISIHVG QAGVQIGNACWELYCLEHGIQPDGQM-PDS------FNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLF HPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYG KKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSS ITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKY MACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEA WARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVE..* >P1;tetrahymena sequence:tetrahymena: : : : ::: 0.00: 0.00 MREVISIHVGQGGIQVGNACWELFCLEHGI------QPDG--QMDAFNTFFSETGAGKHVPRAVFLDLEPTVIDE VRTGTYRQLFHPEQLISGKEDAANNFARGHYTIGKEIVDLCLDRIRKLADNCTGLQGFLVFNSVGGGTGSGLGSL LLERLSVDYGKKSKLGFTIYPSPQVSTAVVEPYNSILSTHSLLEHTDVAVMLDNEAIYDICRRNLDIERPTYTNL NRLIAQVISSLTASLRFDGALNVDITEFQTNLVPYPRIHFMLSSYAPIISAEKAYHEQLSVAEITNSAFEPANMM AKCDPRHGKYMACSMMYRGDVVPKDVNASIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVMRAVCM ISNSTAIAEVFSRLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGIETAE./MREIVHIQGG QCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGRYVPRAILMDLEPGTMDSVRAGPFGQLF RPDNFVFGQTGAGNNWAKGHYTEGAELIDSVLDVVRKEAEGCDCLQGFQITHSLGGGTGSGMGTLLISKVREEYP DRIMETFSVVPSPKVSDTVVEPYNATLSVHQLVENADECMVIDNEALYDICFRTLKLTTPTYGDLNHLVSAAMSG VTCCLRFPGQLNSDLRKLAVNLIPFPRLHFFMIGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMCAADPRHGRY LTASALFRGRMSTKEVDEQMLNVQNKNSSYFVEWIPNNIKSSICDIPPK--------GLKMAVTFVGNSTAIQEM FKRVAEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQ-DAT-..* I'm getting this error "ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 864 861 For alignment entry: 1 3jar_template". Thanks a lot.

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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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