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
Adriana Esteves wrote: > 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?
env.io.hetatm=True only tells Modeller to read non-water HETATM residues. To read water as well, set env.io.water=True too.
Once you do this, you will also need to change your alignment, adding a 'w' residue to the template sequence for every water in the PDB.
> Can I copy the waters coordinates from de template file to the > modelled one
Sure - if you want waters in your model too, add a 'w' residue in your alignment to the model sequence, aligned to the water you want to copy in the template sequence.
It is rare to actually include waters in comparative models, as they generally don't add any useful information. If you have crystallographic waters, however, it may be useful to include them, although you may need to construct sensible restraints to your protein.
Ben Webb, Modeller Caretaker
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Modeller Caretaker