October 2022 - modeller_usage

Multichain model
by amirbazrafshan1375＠gmail.com 17 Oct '22

17 Oct '22

I'm currently using multi-chain modeller script to build a hetero-dimer protein complex but I faced to this error and I can't fix it. It is just for practice so I choose a simple dimer protein and mutated the sequence but the sequence length between .ali file and the pdb file of the template is similar. ( There is no such chain B, modeller.ModellerError: define__595E> Number of selected atoms in sets 2 & 3 is not the same: 109 118) These are alignment file and scripts that I used: a) Alignment file: ****I used align2d script to build alignment file. from modeller import * env = Environ() aln = Alignment(env) mdl = Model(env, file='temp', model_segment=(('FIRST:A','LAST:B'))) aln.append_model(mdl, align_codes='temp', atom_files='temp.pdb') aln.append(file='Target.ali', align_codes='target') aln.align2d(max_gap_length=50) aln.write(file='target-temp2.ali', alignment_format='PIR') aln.write(file='target-temp2.pap', alignment_format='PAP')*** And the alignment file would be like this: ****>P1;template structureX:file.pdb:1:A:+227:B::: 2.30:-1.00 EIVLTQSPGTLSLSPGERATLSCRASQSVGSSYLAWYQQKPGQAPRLLIYGAFSRATGIPDRFSGSGSGTDFTLT ISRLEPEDFAVYYCQQYGSSPWTFGQGTKVEIKR/QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYTMHWVRQA PGKGLEWVTFISYDGNNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAIYYCARTGWLGPFDYWGQGTLVT VSS* >P1;target sequence:target:: :: ::: 0.00: 0.00 EIVLTQSPGSLSLSPGERATLSCRASQSVGSSYLAWFQQKPGQAHRLLIYGAFSRATGIPDRFSGSDSGTDFTLT ISRLEPEDFAAYYCQQYGSSPWTFGQGTKVEIKR-QVQLVESGGGVVQPHRSLRLSCAASGFTFSSYTMHWVRQA PGKGLEWVEFISYDGNNKYYADSVKGRFTITRDNSKNTLYLQMNSLRAEDTAIYYCARTGWLGPYDYWGQPTLVTVSS* b) Building the model: To build a multi-chain model I've tried this script as it's mentioned in the modeller manual: *** from modeller import * from modeller.automodel import * log.verbose() class MyModel(AutoModel): def special_restraints(self, aln): s1 = Selection(self.chains['A']).only_atom_types('CA') s2 = Selection(self.chains['B']).only_atom_types('CA') self.restraints.symmetry.append(Symmetry(s1, s2, 1.0)) def user_after_single_model(self): self.restraints.symmetry.report(1.0) env = Environ() env.io.atom_files_directory = ['.', '../atom_files'] a = MyModel(env, alnfile = 'target-temp2.ali' , knowns = 'temp', sequence = 'target') a.starting_model= 1 a.ending_model = 2 a.make() ***** After run the script I see this error: (No such chain: B) I was practicing before with other protein and when I saw this error I changed the alignment file (......TKVEIKR-QVQLVES......) to (.......TKVEIKR/QVQLVES........) and the problem solved. But here when I change (-) to (/) for the target sequence in alignment file I get another error : (modeller.ModellerError: define__595E> Number of selected atoms in sets 2 & 3 is not the same: 109 118) Could you please help me? I have no idea about this error. And I have another question. Is it possible to build a single polypeptide chain model with multi-chain approach? Is there a way to combine multi-chain script with multi-template script to keep the orientation of the different protein domains?

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Loop Refining Multiple Model Failure Inquiry
by Joel Subach 05 Oct '22

05 Oct '22

Hello, for the above topic I can not seem to generate more than 1-model, although my script indicates 500 models. I have tried using refine.very_fast and refine.slow and moreover tried with different residue amounts for my heptamer ranging from 84 residues (12/chain) up to 126 residues (18/chain). Maybe I can only encode up to 12 residues in total per script? Thanks:) Joel

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Homomultimer modeling
by Franceschini Ghilardi, Amanda (BIDMC - Lijun Sun - General Surg SF) 04 Oct '22

04 Oct '22

Hi, I am trying to model a heptamer (homomultimer), but the structure generated is wrong because there are many clashes and it looks completely different from the template. How can I solve this issue? Please, see my files and scripts below. The .ali for the alignment was edited by repeating the sequence seven times and separating each sequence by "/" >P1;name Sequence:name:::::::: XXXXX/XXXXX/XXXXX/XXXXX* The alignment script from modeller import * env = Environ() aln = Alignment(env) mdl = Model(env, file='template', model_segment=('FIRST:A','LAST:F')) aln.append_model(mdl, align_codes='template', atom_files='template.pdb') aln.append(file='target.ali', align_codes='target') aln.align2d(max_gap_length=50) aln.write(file='aligned.ali', alignment_format='PIR') aln.write(file='aligned.pap', alignment_format='PAP') The script to build the model from modeller import * from modeller.automodel import * #from modeller import soap_protein_od 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') s6 = Selection(self.chains['F']).only_atom_types('CA') self.restraints.symmetry.append(Symmetry(s1, s2, 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) 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 = 'aligned.ali' , # alignment filename knowns = 'template', # codes of the templates sequence = 'target', assess_methods=(assess.DOPE)) # code of the target 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 # Get a list of all succesfully built models from a.output ok_models = [x for x in a.outputs if x['failure'] is None] # Rank the models by DOPE score key = 'DOPE score' if sys.version_info[:2] == (2,3): ok_models.sort(lambda a,b: cmp(a[key], b[key])) else: ok_models.sort(key=lambda a: a[key])

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Re: Homomultimer modeling
by Joel Subach 01 Oct '22

01 Oct '22

Hello I would first need to be sure that you selected the correct template(s) accordingly if you want please send me your protein heptamer query and the template(s) you selected and how you discovered these templates. (I completed my Doctoral Dissertation on modeling an unknown heptamer.) Thanks:) Joel On Sat, Oct 1, 2022 at 9:51 AM Joel Subach <mjsubach(a)alumni.ncsu.edu> wrote: > > > ---------- Forwarded message --------- > From: <modeller_usage-owner(a)salilab.org> > Date: Sat, Oct 1, 2022 at 9:32 AM > Subject: Re: [modeller_usage] Homomultimer modeling > To: <mjsubach(a)alumni.ncsu.edu> > > > Your message to the modeller_usage mailing-list was rejected for the > following > reasons: > > The message is not from a list member > > The original message as received by Mailman is attached. > > > > ---------- Forwarded message ---------- > From: Joel Subach <mjsubach(a)alumni.ncsu.edu> > To: "Franceschini Ghilardi, Amanda (BIDMC - Lijun Sun - General Surg SF)" < > afrance2(a)bidmc.harvard.edu> > Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> > Bcc: > Date: Sat, 1 Oct 2022 09:32:25 +0200 > Subject: Re: [modeller_usage] Homomultimer modeling > Hello I would first need to be sure that you selected the correct > template(s) accordingly if you want please send me your protein heptamer > query and the template(s) you selected and how you discovered these > templates. (I completed my Doctoral > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > > ZjQcmQRYFpfptBannerEnd > Hello I would first need to be sure that you selected the correct > template(s) accordingly if you want please send me your protein heptamer > query > and the template(s) you selected and how you discovered these templates. > (I completed my Doctoral Dissertation on modeling an unknown heptamer.) > > Thanks:) > Joel > > On Fri, Sep 30, 2022 at 11:51 PM Franceschini Ghilardi, Amanda (BIDMC - > Lijun Sun - General Surg SF) via modeller_usage < > modeller_usage(a)salilab.org> wrote: > >> Hi, I am trying to model a heptamer (homomultimer), but the structure >> generated is wrong because there are many clashes and it looks completely >> different from the template. How can I solve this issue? Please, see my >> files and scripts below. >> ZjQcmQRYFpfptBannerStart >> This Message Is From an External Sender >> This message came from outside your organization. >> >> ZjQcmQRYFpfptBannerEnd >> Hi, >> >> I am trying to model a heptamer (homomultimer), but the structure >> generated is wrong because there are many clashes and it looks completely >> different from the template. How can I solve this issue? Please, see my >> files and scripts below. >> >> The .ali for the alignment was edited by repeating the sequence seven >> times and separating each sequence by "/" >> >P1;name >> Sequence:name:::::::: >> XXXXX/XXXXX/XXXXX/XXXXX* >> >> The alignment script >> from modeller import * >> >> env = Environ() >> aln = Alignment(env) >> mdl = Model(env, file='template', model_segment=('FIRST:A','LAST:F')) >> aln.append_model(mdl, align_codes='template', atom_files='template.pdb') >> aln.append(file='target.ali', align_codes='target') >> aln.align2d(max_gap_length=50) >> aln.write(file='aligned.ali', alignment_format='PIR') >> aln.write(file='aligned.pap', alignment_format='PAP') >> >> The script to build the model >> from modeller import * >> from modeller.automodel import * >> #from modeller import soap_protein_od >> >> 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') >> s6 = Selection(self.chains['F']).only_atom_types('CA') >> self.restraints.symmetry.append(Symmetry(s1, s2, 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) >> >> 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 = 'aligned.ali' , # alignment filename >> knowns = 'template', # codes of the templates >> sequence = 'target', >> assess_methods=(assess.DOPE)) # code of the target >> >> >> 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 >> >> # Get a list of all succesfully built models from a.output >> ok_models = [x for x in a.outputs if x['failure'] is None] >> >> # Rank the models by DOPE score >> key = 'DOPE score' >> if sys.version_info[:2] == (2,3): >> ok_models.sort(lambda a,b: cmp(a[key], b[key])) >> else: >> ok_models.sort(key=lambda a: a[key]) >> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage(a)salilab.org >> https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ >> >

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