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 wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww wwwwwwwwwwwwwwwwwwwwwwwwwwwwwww* >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.
On 5/12/21 6:18 PM, MARIANA BRANDI MENDONÇA PINHEIRO wrote: > I am having a problem with ligand generation. ... > The ligand is chain X at 2q3z = /.P.LPF./ > The models are created but without chain B/X or any ligand/polypeptide.
In order for the ligand to appear in the model, you must also include the '.' residue in your target (the 'sequence' entry in the alignment, P21980 in your case) and align it with the ligand in one of the templates. See also the example alignment align-ligand.ali at https://salilab.org/modeller/10.1/manual/node18.html
Ben Webb, Modeller Caretaker