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
|
This Message Is From an External Sender
This message came from outside your organization.
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
|