Using the scritp model-ligand.py I introduced a ligand in my model, but the waters were no added. Did I omitted anything in the alignment? Can I copy the waters coordinates from de template file to the modelled one and .... I don't know what to do then, but I something can be done!! This is the script and this the alignment # 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 = 'align-ligand.ali', # alignment filename knowns = '1O8v', # codes of the templates sequence = 'EgFABP2') # code of the target a.starting_model= 4 # index of the first model a.ending_model = 4 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling
C; >P1;1O8v structureX:1O8v:1 :A :134 : :EgFABP1 :Echinococcus granulosus: : MEAFLGTWKMEKSEGFDKIMERLGVDFVTRKMGNLVKPNLIVTDLGGGKYKMRSESTFKT TE.S-FKLGEKFKEVTPDSREVASLITVENGVMKHEQDDKTKVTYIERVVEGNELKATVKV DEVVCVRTYSKVA.*
>P1;EgFABP2 sequence:EgFABP2:1 : :134 : :EgFABP2:Echinococcus granulosus: : MEPFIGTWKMEKSEGFDKIMERLGVDYFTRKMGNMMKPNLIISDLGDGRYNMRSESKFKT SE-FSFKLGEQFKEVTPDSREVMSMLTVEDGVLKQEQVGKDKTTYIDRVVDGNELRATVKA DELVCVRTYSKRM.*
Dra. A. Esteves Secc. Bioquímica Faculty of Sciences Iguá 4225-Montevideo URUGUAY tel.(5982)525 2095 fax (5982)525 8617