- modeller_usage - salilab.org

Question on select_atoms vs. select_loop_atoms
by Wiley, Brian 12 Feb '23

12 Feb '23

Hi, When I write a new class that extends either AutoModel or AllHModel and I define the select_atoms() function only the atoms in those residues are modeled and the rest remain at their start position. However when extending LoopModel and write the same selection for select_loop_atoms(), all the atoms move. Is this intended by design? Brian Wiley Bioinformatics Scientist / Learner Washington University in St. Louis p. 480-370-4230 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found
by Irawati Roy 10 Feb '23

10 Feb '23

Hello I am trying to build a model of a protein sequence where I have structure of two domains of the protein as an input. One structure is collected from PDB. another is simulation generated. I got the following error: Traceback (most recent call last): File "align1.py", line 7, in <module> mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:A')) File "/usr/lib/python3.8/dist-packages/modeller/model.py", line 101, in __init__ self.read(**vars) File "/usr/lib/python3.8/dist-packages/modeller/model.py", line 151, in read return _modeller.mod_model_read2(self.modpt, io.modpt, _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " FIRST", chain " A"; atom file name: A1.pdb The simulation generated structure file looks like following: ATOM 1 N MET X 1 43.720 45.860 63.480 0.00 0.00 ATOM 2 H1 MET X 1 44.460 45.570 64.150 0.00 0.00 ATOM 3 H2 MET X 1 42.750 45.730 63.840 0.00 0.00 ATOM 4 H3 MET X 1 43.890 45.180 62.720 0.00 0.00 ATOM 5 CA MET X 1 43.900 47.280 63.110 0.00 0.00 ATOM 6 HA MET X 1 43.520 47.850 63.950 0.00 0.00 ATOM 7 CB MET X 1 45.340 47.790 62.980 0.00 0.00 ATOM 8 HB1 MET X 1 45.450 48.870 62.740 0.00 0.00 The code used is the following: from modeller import * env = environ() aln = alignment(env) env.io.hetatm = True for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:X')) aln.append_model(mdl, atom_files=pdb, align_codes=pdb) aln.append(file='query1.ali', align_codes='query') aln.malign() aln.write(file='querytemplate_new.ali', alignment_format='PIR') aln.write(file='querytemplate_new.pap', alignment_format='PAP') Any help regarding how to solve this error will be great. Thanks Ira

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Error: No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT
by irawatiroy＠gmail.com 10 Feb '23

10 Feb '23

Dear Users Hello I am trying to build a model of a protein sequence where I have structures of two domains of the same protein as an input. One structure is collected from PDB. another is simulation generated. I got the following error: Traceback (most recent call last): File "align1.py", line 7, in <module> mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:A')) File "/usr/lib/python3.8/dist-packages/modeller/model.py", line 101, in __init__ self.read(**vars) File "/usr/lib/python3.8/dist-packages/modeller/model.py", line 151, in read return _modeller.mod_model_read2(self.modpt, io.modpt, _modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " FIRST", chain " A"; atom file name: A1.pdb The simulation generated structure file looks like following: ATOM 1 N MET X 1 43.720 45.860 63.480 0.00 0.00 ATOM 2 H1 MET X 1 44.460 45.570 64.150 0.00 0.00 ATOM 3 H2 MET X 1 42.750 45.730 63.840 0.00 0.00 ATOM 4 H3 MET X 1 43.890 45.180 62.720 0.00 0.00 ATOM 5 CA MET X 1 43.900 47.280 63.110 0.00 0.00 ATOM 6 HA MET X 1 43.520 47.850 63.950 0.00 0.00 ATOM 7 CB MET X 1 45.340 47.790 62.980 0.00 0.00 ATOM 8 HB1 MET X 1 45.450 48.870 62.740 0.00 0.00 ATOM 9 HB2 MET X 1 45.800 47.630 63.980 0.00 0.00 ATOM 10 CG MET X 1 46.250 47.060 61.990 0.00 0.00 ATOM 11 HG1 MET X 1 47.240 47.350 62.410 0.00 0.00 ATOM 12 HG2 MET X 1 46.180 45.950 62.040 0.00 0.00 ATOM 13 SD MET X 1 46.260 47.620 60.260 0.00 0.00 ATOM 14 CE MET X 1 47.960 47.000 60.080 0.00 0.00 ATOM 15 HE1 MET X 1 47.960 45.900 60.270 0.00 0.00 ATOM 16 HE2 MET X 1 48.350 47.180 59.060 0.00 0.00 ATOM 17 HE3 MET X 1 48.640 47.540 60.770 0.00 0.00 ATOM 18 C MET X 1 43.020 47.620 61.960 0.00 0.00 ATOM 19 O MET X 1 42.650 46.780 61.140 0.00 0.00 ATOM 20 N ALA X 2 42.710 48.920 61.800 0.00 0.00 ATOM 21 HN ALA X 2 43.190 49.580 62.370 0.00 0.00 ATOM 22 CA ALA X 2 42.060 49.460 60.650 0.00 0.00 ATOM 23 HA ALA X 2 41.530 48.650 60.160 0.00 0.00 ATOM 24 CB ALA X 2 41.310 50.730 61.090 0.00 0.00 ATOM 25 HB1 ALA X 2 41.940 51.410 61.700 0.00 0.00 The code used is the following: from modeller import * env = environ() aln = alignment(env) env.io.hetatm = True for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:X')) aln.append_model(mdl, atom_files=pdb, align_codes=pdb) aln.append(file='query1.ali', align_codes='query') aln.malign() aln.write(file='querytemplate_new.ali', alignment_format='PIR') aln.write(file='querytemplate_new.pap', alignment_format='PAP') Any help regarding how to solve this error will be great. Thanks Ira

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Generating chimeric protein from templates
by Ta-Chou Huang 06 Feb '23

06 Feb '23

Dear Users, I would like to generate a chimeric protein from templates, especially following the tips from FAQ 1 ( https://salilab.org/modeller/9.10/manual/node36.html) and also here https://salilab.org/modeller/9.10/manual/node21.html. To better understand the code and its meaning, I used two simple sequences together as test case. In pir file, it has: >P1;2xkmA structureN:2xkm GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA -------------------------------------------* >P1;4xknE structureX:4xkh ---------------------------------------------- NGLSEDEALQRALELSLAEAKPQVLSSQEEDDLALAQALSASE* >P1;test sequence:test GVIDTSAVESAITDGQGDMKAIGGYIVGALVILAVAGLIYSMLRKA NGLSEDEALQRALELSLAEAKPQVLSSQEEDDLALAQALSASE* and almost the same for ali file. However, using the build_profile.py, it shows the first error: _modeller.FileFormatError: parse_pir__E> Invalid PIR file header line: structureN:2xkm There should be 10 fields separated by colons, : This line actually contains 2 fields. Now here comes my question, from the FAQ, I thought it was enough to use two fields for the template? Even when I put enough colon to make it as 10 fields, it shows the next error that it could not find the PDB file. To fix this problem, I tried to put the entire information of the structureN (and structureX) line from the pdb_95.pir which I download from the Modeller website, with the same build_profile.py, the third error comes: _modeller.StatisticsError: regress_657E> Not enough bins in histogram - cannot calculate statistics, nbins: 1 In the end, I don't understand the exact problem to cause all these errors, did miss something in the pir or ali file? or I used the wrong script. Hope to hear any suggestions from you. Best wishes.

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Question about the loop modeling
by Ecem Güngör 07 Dec '22

07 Dec '22

Hello, I have an X-ray structure where I want to model some loop regions. However, while modeling these loops, I do not want to either optimize or refine them. How should I proceed for that? Any help would be appreciated.

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Modeller 10.4 release
by Modeller Caretaker 03 Nov '22

03 Nov '22

A new version of Modeller, 10.4, 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 9 or 10, there is no need to reregister for Modeller 10.4 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.4 is a minor update that supports residue names longer than three characters in mmCIF files, fixes an issue with the mod10.4 compatibility script on macOS Ventura 13 or later on Apple Silicon (ARM64/M1) machines, and adds support for Python 3.11 (and once conda and brew themselves support it, Modeller conda/brew packages will be made available for 3.11). If you encounter bugs in Modeller 10.4, please see https://salilab.org/modeller/10.4/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 unsubscribe from the modeller_announce mailing list, or 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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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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