modeller_usage

modeller_usage@salilab.org

4 participants
3146 discussions

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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Missing Residue and Loop Modeling Script Inquiry for an OLIGOMER
by Joel Subach 24 Sep '22

24 Sep '22

Hello, for the above topic I have a heptamer, accordingly should my missing residue code for chains A-G be just and A-chain indication with the B-G being modeled via default or should I designate each chain, see below: return Selection(self.residue_range(`88:A´, `100:A´)) or return Selection(self.residue_range('88:A', '100:A'), self.residue_range('88:B', '100:B'), self.residue_range('88:C', '100:C'), self.residue_range('88:D', '100:D'), self.residue_range('88:E', '100:E'), self.residue_range('88:F', '100:F'), self.residue_range('88:G', '100:G')) I tried the later (A-G coding) and received the below error where there should be this missing residue? *raise KeyError("No such %s: %s" % (indxtyp, indx))* *KeyError: 'No such residue: 88:B'*

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Oligomer Missing Loop Residue Restrained Modeling, Broken Loop Issue
by Joel Subach 23 Sep '22

23 Sep '22

Hi, I loop missing residue MODELLER modeled a heptamer both unrestrained and restrained with the former exhibiting an RMSD of 0.295 while the restrained exhibited an RMSD of 0.0. The restrained model´s missing residue loops, however, are too dynamic and seem to be broken when visualized via Pymol. Accordingly, is there a way to generate the restrained version to exhibit intact loops so that I may keep this version because of its 0.0 RMSD? Thanks if you can help:) Below is the code I used: *from modeller import *from modeller.automodel import * # Load the AutoModel classlog.verbose()env = Environ()# directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files']class MyModel(AutoModel): def select_atoms(self): return Selection(self.residue_range('89:A', '99:A'))a = MyModel(env, alnfile = 'alignment.ali', knowns = '7dwb', sequence = '7dwb_fill')a.starting_model= 1a.ending_model = 1a.make()*

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Generating a model using multiple templates with different ligands
by Franceschini Ghilardi, Amanda (BIDMC - Lijun Sun - General Surg SF) 20 Sep '22

20 Sep '22

Hi, I have been trying to generate a model of the AhR using three different templates with different ligands in each of them. When I submit the script for the model building, I get the error below: "_modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 110 109 For alignment entry: 1 3f1o_pasA" I tried changing the number highlighted in the alignment file to 110, but the same error appeared. Was I supposed to change anything in the pdb file? Also, since I would like to consider the three ligands, is that correct to add three dots at the end of the alignment and pap file? The alignment, .pap, and script for the model building are below. Model building script: # Comparative modeling with ligand transfer from the template from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the AutoModel class import sys log.verbose() # request verbose output env = Environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True a = AutoModel(env, alnfile='ahr-mult.ali', knowns=('3f1o_pasA','3h7w_pasA','3h82_pasA'), sequence='AhR', assess_methods=(assess.DOPE)) 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 the actual comparative modeling Alignment file: >P1;3f1o_pasA structureX:3f1o_pas_fit.pdb:236:A:+109:A:MOL_ID 1; MOLECULE ENDOTHELIAL PAS DOMAIN-CONTAINING PROTEIN 1; CHAIN A; FRAGMENT HIF2 ALPHA C-TERMINAL PAS DOMAIN; SYNONYM EPAS-1, MEMBER OF PAS PROTEIN 2, BASIC-HELIX-LOOP- PROTEIN MOP2, HYPOXIA-INDUCIBLE FACTOR 2 ALPHA, HIF-2 ALPHA ALPHA, HIF-1 ALPHA-LIKE FACTOR, HLF; ENGINEERED YES; MUTATION YES; MOL_ID 2; MOLECULE ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR; CHAIN B; FRAGMENT ARNT C-TERMINAL PAS DOMAIN; SYNONYM ARNT PROTEIN, DIOXIN RECEPTOR, NUCLEAR TRANSLOCATO HYPOXIA-INDUCIBLE FACTOR 1 BETA, HIF-1 BETA; ENGINEERED YES; MUTATION YES:MOL_ID 1; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_COMMON HUMAN; ORGANISM_TAXID 9606; GENE EPAS1, HIF2A, HYPOXIA INDUCIBLE FACTOR 2 ALPHA, MOP2; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; EXPRESSION_SYSTEM_STRAIN BL21; EXPRESSION_SYSTEM_VECTOR_TYPE PHIS-GB1-PARALLEL; MOL_ID 2; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_COMMON HUMAN; ORGANISM_TAXID 9606; GENE ARNT, ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; EXPRESSION_SYSTEM_STRAIN BL21; EXPRESSION_SYSTEM_VECTOR_TYPE PHIS-PARALLEL: 1.60: 0.17 -FKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGR-SAYEFYHALDSENMTKSHQNLCTKGQVVSGQYR MLAKHGGYVWLETQGTVIYN-----PQCIMCVNYVLSEIEK.* >P1;3h7w_pasA structureX:3h7w_pas_fit.pdb:236:A:+108:A:MOL_ID 1; MOLECULE ENDOTHELIAL PAS DOMAIN-CONTAINING PROTEIN 1; CHAIN A; FRAGMENT HIF2ALPHA C-TERMINAL PAS DOMAIN (UNP RESIDUES 239 SYNONYM EPAS-1, MEMBER OF PAS PROTEIN 2, BASIC-HELIX-LOOP- PROTEIN MOP2, HYPOXIA-INDUCIBLE FACTOR 2 ALPHA, HIF-2 ALPHA ALPHA, HIF-1 ALPHA-LIKE FACTOR, HLF; ENGINEERED YES; MUTATION YES; MOL_ID 2; MOLECULE ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR; CHAIN B; FRAGMENT ARNT C-TERMINAL PAS DOMAIN (UNP RESIDUES 356 TO 4 SYNONYM ARNT PROTEIN, CLASS E BASIC HELIX-LOOP-HELIX PROTE BHLHE2, DIOXIN RECEPTOR, NUCLEAR TRANSLOCATOR, HYPOXIA-INDU FACTOR 1 BETA, HIF-1 BETA; ENGINEERED YES; MUTATION YES:MOL_ID 1; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_COMMON HUMAN; ORGANISM_TAXID 9606; GENE EPAS1, HIF2A, HYPOXIA INDUCIBLE FACTOR 2 ALPHA, MOP2; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; EXPRESSION_SYSTEM_STRAIN BL21(DE3); EXPRESSION_SYSTEM_VECTOR_TYPE PLASMID; EXPRESSION_SYSTEM_PLASMID PHIS-GB1-HIF2APAS-B; MOL_ID 2; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_COMMON HUMAN; ORGANISM_TAXID 9606; GENE ARNT, ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR, EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; EXPRESSION_SYSTEM_STRAIN BL21(DE3); EXPRESSION_SYSTEM_VECTOR_TYPE PLASMID; EXPRESSION_SYSTEM_PLASMID PHIS-GB1-ARNT-PAS-B: 1.65: 0.20 -FKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGR-SAYEFYHALDSENMTKSHQNLCTKGQVVSGQYR MLAKHGGYVWLETQGTVIY------PQCIMCVNYVLSEIEK.* >P1;3h82_pasA structureX:3h82_pas_fit.pdb:-1:A:+115:A:MOL_ID 1; MOLECULE ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR; CHAIN B; FRAGMENT ARNT C-TERMINAL PAS DOMAIN (UNP RESIDUES 356 TO 4 SYNONYM ARNT PROTEIN, CLASS E BASIC HELIX-LOOP-HELIX PROTE BHLHE2, DIOXIN RECEPTOR, NUCLEAR TRANSLOCATOR, HYPOXIA-INDU FACTOR 1 BETA, HIF-1 BETA; ENGINEERED YES; MUTATION YES; MOL_ID 2; MOLECULE ENDOTHELIAL PAS DOMAIN-CONTAINING PROTEIN 1; CHAIN A; FRAGMENT HIF2ALPHA C-TERMINAL PAS DOMAIN (UNP RESIDUES 239 SYNONYM EPAS-1, MEMBER OF PAS PROTEIN 2, BASIC-HELIX-LOOP- PROTEIN MOP2, HYPOXIA-INDUCIBLE FACTOR 2 ALPHA, HIF-2 ALPHA ALPHA, HIF-1 ALPHA-LIKE FACTOR, HLF; ENGINEERED YES; MUTATION YES:MOL_ID 1; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_COMMON HUMAN; ORGANISM_TAXID 9606; GENE ARNT, ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR, EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; EXPRESSION_SYSTEM_STRAIN BL21(DE3); EXPRESSION_SYSTEM_VECTOR_TYPE PLASMID; EXPRESSION_SYSTEM_PLASMID PHIS-GB1-ARNT-PAS-B; MOL_ID 2; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_COMMON HUMAN; ORGANISM_TAXID 9606; GENE EPAS1, HIF2A, HYPOXIA INDUCIBLE FACTOR 2 ALPHA, MOP2; EXPRESSION_SYSTEM ESCHERICHIA COLI; EXPRESSION_SYSTEM_TAXID 562; EXPRESSION_SYSTEM_STRAIN BL21(DE3); EXPRESSION_SYSTEM_VECTOR_TYPE PLASMID; EXPRESSION_SYSTEM_PLASMID PHIS-GB1-HIF2APAS-B: 1.50: 0.20 EFKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGR-SAYEFYHALDSENMTKSHQNLCTKGQVVSGQYR MLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEK.* >P1;AhR sequence:AhR:: :: :::-1.00:-1.00 EIR-TKNFIFRTKHKLDFTPIGCDAKGRIVLGYTEAELCTRGSGYQFIHAADMLYCAESHIRMIKTGESGMIVFR LLTKNNRWTWVQSNARLLYK--NGRPDYIIVTQRPLTDEEG...* pap file: _aln.pos 10 20 30 40 50 60 3f1o_pasA -FKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGR-SAYEFYHALDSENMTKSHQNLCTKG 3h7w_pasA -FKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGR-SAYEFYHALDSENMTKSHQNLCTKG 3h82_pasA EFKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGR-SAYEFYHALDSENMTKSHQNLCTKG AhR EIR-TKNFIFRTKHKLDFTPIGCDAKGRIVLGYTEAELCTRGSGYQFIHAADMLYCAESHIRMIKTG _consrvd * * * ** ** ** * * * * ** * ** * _aln.pos 70 80 90 100 110 3f1o_pasA QVVSGQYRMLAKHGGYVWLETQGTVIYN-----PQCIMCVNYVLSEIEK/.-- 3h7w_pasA QVVSGQYRMLAKHGGYVWLETQGTVIY------PQCIMCVNYVLSEIEK/.-- 3h82_pasA QVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEK/.-- AhR ESGMIVFRLLTKNNRWTWVQSNARLLYK--NGRPDYIIVTQRPLTDEEG/... _consrvd * * * * * * * * * Best Regards, Amanda F. Ghilardi

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Missing Residue Modeling for an Oligomer Inquiry
by Joel Subach 19 Sep '22

19 Sep '22

Hello, I missing residue modeled a loop region of a monomer from an oligomer heptamer and then oligomerized this new model monomer via GalaxyWeb into a heptamer, however, the generated heptamer´s RMSD to the PDB structure is a great 40 A. My understanding is that my above methodology is how Modeller would function best due to interfacing of multiple subunit problems if I tried to missing residue model all seven loops with missing residues. Is it possible to try and missing residue model the complete heptamer regardless due to my generated heptame exhibiting an unsatisfactory RMSD Value? Thanks

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