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@alumni.ncsu.edu wrote:
> > > ---------- Forwarded message --------- > From: modeller_usage-owner@salilab.org > Date: Sat, Oct 1, 2022 at 9:32 AM > Subject: Re: [modeller_usage] Homomultimer modeling > To: mjsubach@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@alumni.ncsu.edu > To: "Franceschini Ghilardi, Amanda (BIDMC - Lijun Sun - General Surg SF)" < > afrance2@bidmc.harvard.edu> > Cc: "modeller_usage@salilab.org" modeller_usage@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@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@salilab.org >> https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ >> >