Respected Sir
i am trying to add my model one zinc HETATM, but my efforts are failed , iam getting ATOM in my file pdb instead HETATM
in the template structure Experimentally solved Residues Region 191-609 , protein Total Length: 419 in that Five residue are Missing Residue
Here i mentioned
Alignment file
>P1;2DW0
structureX:2DW0.pdb: 196 :A:+414 :A:MOL_ID 1; MOLECULE CATROCOLLASTATIN; CHAIN A, B; FRAGMENT RESIDUES 191-609; SYNONYM VAP2, VASCULAR APOPTOSIS-INDUCING PROTEIN-2, CATROCOLLASTATIN/VAP2B:MOL_ID 1; ORGANISM_SCIENTIFIC CROTALUS ATROX; ORGANISM_COMMON WESTERN DIAMONDBACK RATTLESNAKE; ORGANISM_TAXID 8730: 2.15: 0.17
PFRFVELVLVVDKAMVTKNNGDLDKIKTRMYEIVNTVNEIYRYMYIHVALVGLEIWSNEDKITVKPEAGYTLNAF
GEWRKTDLLTRKKHDNAQLLTAIDLD-RVIGLAYVGSMCHPKRSTGIIQDYSEINLVVAVIMAHEMGHNLGINHD
SGYCSCGDYACIMRPEISPEPSTFFSNCSYFECWDFIMNHNPECILNEPLGTDIISPPVCGNELLEVGEECDCGT
PENCQNECCDAATCKLKSGSQCGHGDCCEQCKFSKSGTECRASMSECDPAEHCTGQSSECPADVFHKNGQPCLDN
YGYCYNGNCPIMYHQCYDLFGADVYEAEDSCFERNQKGNYYGYCRKENGNKIPCAPEDVKCGRLYCKDNSPGQNN
PCKMFYSNEDEHKGMVLPGTKCADGKVCSNGHCVDVATAY.*
>P1;TvLDH
sequence:TvLDH: : : : ::: 0.00: 0.00
P-RYIELVIVADRAMVTKNNGDLTAIRTWVHQIVNDMTVMYRDLNIHITLAAVVIWNKRDLITVTSSAEDTLNLF
GTWRETKYLKHRKHDNAQLLTGIILDDDTIGLAYVGGMCDPKKSVGIIEDHSTEHLLVAATMAHEMGHNLGMNHD
ANQCNCGANGCVMSATLTEQTSYQFSDCSKDEYQNYLTDHNPQCILNQPLRTD-T-P-VSRNELLQ-NSAHPC--
--------CDPVTCQPK--RFCVSGPCCENCQFVRAGTVCNPAKGD-WMDDYCTGISSDCPRNPL----------
-----NGFR------------------------------------------------------------------
----------------------------------------.*
and
Model Ligand python script which i used as followed
# Homology modeling with ligand transfer from the template
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class
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 = 'TvLDH-2DW0A.ali', # alignment filename
knowns = '2DW0', # codes of the templates
sequence = 'TvLDH') # code of the target
a.starting_model= 1 # index of the first model
a.ending_model = 5 # index of the last model
# (determines how many models to calculate)
a.make() # do the actual homology modeling
kindly give provide your valuable suggestion regarding error
--
Regards,
S.VENKATESH,