ligand is not generated - modeller_usage

13 May 2021


      I am having a problem with ligand generation.
Alignment file:
>P1;2q3z
structureX:2q3z:1:A:+929:X:MOL_ID  1; MOLECULE  TRANSGLUTAMINASE 2; CHAIN
 A; SYNONYM  TISSUE TRANSGLUTAMINASE, TGASE C, TGC, TGC,
TRANSGLUTAMINASE-2, TGASE- H; EC  2.3.2.13; ENGINEERED  YES; MOL_ID  2;
MOLECULE  POLYPEPTIDE; CHAIN  X; ENGINEERED  YES:MOL_ID  1;
ORGANISM_SCIENTIFIC  HOMO SAPIENS; ORGANISM_COMMON  HUMAN; ORGANISM_TAXID
 9606; GENE  TGM2; EXPRESSION_SYSTEM  ESCHERICHIA COLI;
EXPRESSION_SYSTEM_TAXID  562; MOL_ID  2; SYNTHETIC  YES; OTHER_DETAILS
 CHEMICALLY SYNTHESIZED.: 2.00: 0.23
MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYQASVDSLTFS
VVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLE
ASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPW
NFGQFQDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVGSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHDS--NLLIEYFRN---------SEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQ-------KSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRAN----------HGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLTLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLVPLHMGLHKLVVNFESDKLKAVKGFRNVI----/.P.LPF./.....wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
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>P1;3s3j_L
structureX:3s3j_L:2:A:+782:B:MOL_ID  1; MOLECULE  PROTEIN-GLUTAMINE
GAMMA-GLUTAMYLTRANSFERASE 2; CHAIN  A; FRAGMENT  UNP RESIDUES 2-687;
SYNONYM  TISSUE TRANSGLUTAMINASE, TRANSGLUTAMINASE C, TG(C) TGASE C,
TRANSGLUTAMINASE H, TGASE H, TRANSGLUTAMINASE-2, T EC  2.3.2.13; ENGINEERED
 YES; MOL_ID  2; MOLECULE  PEPTIDE INHIBITOR; CHAIN  B; ENGINEERED
 YES:MOL_ID  1; ORGANISM_SCIENTIFIC  HOMO SAPIENS; ORGANISM_COMMON  HUMAN;
ORGANISM_TAXID  9606; GENE  TGM2; EXPRESSION_SYSTEM  ESCHERICHIA COLI;
EXPRESSION_SYSTEM_TAXID  562; MOL_ID  2; SYNTHETIC  YES;
ORGANISM_SCIENTIFIC  SYNTHETIC CONSTRUCT; ORGANISM_TAXID  32630: 2.25: 0.22
-AEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFEDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVVSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAH----NLLIEYFRN---------SEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTP-----GTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQ-------KSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANH---------TGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLNLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLLPLHMGLHKLVVNFESDKLKAVKGFRNVIIG--/-------/.......wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww/w*
>P1;P21980
sequence:P21980: FIRST :A:LAST :B:::0.00:0.00
MAEELVLERCDLELETNGRDHHTADLCREKLVVRRGQPFWLTLHFEGRNYEASVDSLTFSVVTGPAPSQEAGTKARFPLRDAVEEGDWTATVVDQQDCTLSLQLTTPANAPIGLYRLSLEASTGYQGSSFVLGHFILLFNAWCPADAVYLDSEEERQEYVLTQQGFIYQGSAKFIKNIPWNFGQFEDGILDICLILLDVNPKFLKNAGRDCSRRSSPVYVGRVVSGMVNCNDDQGVLLGRWDNNYGDGVSPMSWIGSVDILRRWKNHGCQRVKYGQCWVFAAVACTVLRCLGIPTRVVTNYNSAHDQNSNLLIEYFRNEFGEIQGDKSEMIWNFHCWVESWMTRPDLQPGYEGWQALDPTPQEKSEGTYCCGPVPVRAIKEGDLSTKYDAPFVFAEVNADVVDWIQQDDGSVHKSINRSLIVGLKISTKSVGRDEREDITHTYKYPEGSSEEREAFTRANHLNKLAEKEETGMAMRIRVGQSMNMGSDFDVFAHITNNTAEEYVCRLLLCARTVSYNGILGPECGTKYLLNLNLEPFSEKSVPLCILYEKYRDCLTESNLIKVRALLVEPVINSYLLAERDLYLENPEIKIRILGEPKQKRKLVAEVSLQNPLPVALEGCTFTVEGAGLTEEQKTVEIPDPVEAGEEVKVRMDLLPLHMGLHKLVVNFESDKLKAVKGFRNVIIGPA/-------*
The ligand is chain X at 2q3z = /.P.LPF./
The models are created but without chain B/X or any ligand/polypeptide.
The script:
from modeller import *
from modeller.automodel import *    # Load the automodel class
log.verbose()
env = environ()
#Considering heteroatoms and waters molecules
env.io.hetatm = env.io.water = True
# Directories with input atom files:
#env.io.atom_files_directory = './:../atom_files'
env.io.atom_files_directory = ['./', '../atom_files']
a = MyModel(env,
            alnfile = 'aln-all.ali' , # alignment filename
            knowns  =('2q3z', #sequences
                      '3s3j_L'
     ),       # codes of the templates
            sequence = 'P21980', # code of the target
   assess_methods=(assess.DOPE, assess.normalized_dope, assess.GA341)
#assess model with DOPE
   )
a.starting_model= 1                # index of the first model
a.ending_model  = 3                # index of the last model
Regards,
Mariana.