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