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Re: [modeller_usage] Filling in Missing atoms for a docking complex

Good o know about those options. I was just skimming through section 2
in the manual over lunch and I came across this example script. Would
this also work? If so, are there any advantages to using

2.2.9 Using your own initial model
Normally, automodel generates an initial model by transferring
coordinates from the templates. However, if you
have a prepared PDB file containing an initial model, you can have
automodel use this instead with the inifile
keyword, as in the example below. (This automatically sets
automodel.generate method to generate.read xyz for
you, which is necessary for this to work.)
Example: examples/automodel/model-myini.py
# Modeling using a provided initial structure file (inifile)
from modeller import *
from modeller.automodel import * # Load the automodel class
env = environ()
# directories for input atom files
env.io.atom_files_directory = [’.’, ’../atom_files’]
a = automodel(env,
alnfile = ’alignment.ali’, # alignment filename
knowns = ’5fd1’, # codes of the templates
sequence = ’1fdx’, # code of the target
inifile = ’my-initial.pdb’) # use ’my’ initial structure
a.starting_model= 1 # index of the first model
a.ending_model = 1 # index of the last model
# (determines how many models to calculate)
a.make() # do homology modeling

On Wed, Apr 1, 2009 at 12:15 PM, Modeller Caretaker
<> wrote:
> Jack Shultz wrote:
>> I am new to modeller and I have not gone through the tutorial yet. I
>> have submitted a couple of FASTA format files to mod web. I am would
>> like to fix a problem with my docking complexes I get from autodock.
>> Some of them are missing atoms in a given residue. It was suggested I
>> either use Deep-View or Modeller to insert missing atoms. Can modeller
>> indeed achieve this? Are there any existing scripts to perform this?
> Certainly - that is straightforward, and in fact Modeller will do it
> automatically. Just build a homology model using your existing model as
> a template (the alignment will be simply 1:1 since the sequences are the
> same). Use the regular modeling script at
> http://salilab.org/modeller/9v6/manual/node16.html
> If you want to keep the original conformation of part of the system, use
> the script at http://salilab.org/modeller/9v6/manual/node23.html instead.
> You can also use the same technique to fill in entire missing
> *residues*; see http://salilab.org/modeller/wiki/Missing%20residues for
> an example.
>        Ben Webb, Modeller Caretaker
> --
>              http://www.salilab.org/modeller/
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