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[modeller_usage] HOH



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