Using automodel model-full python script,
1. Do we get any changes in side chain conformations or coordinates if the query sequence is perfectly aligned with template sequence at sequence level. Because upon point mutations, there is no change in sequence alignment. Whole query sequence is perfectly aligned with template.
I calculated no. of contacts of wild type residues and mutant residues, there is no change at all. I used only distance between C-alpha atoms(CA) while calculating .
Is there any change in side chain conformations in the modeled structures by using this script.
2. Can I get to know the details of a.make() and a.auto_align() commands used in this script. I WANT TO KNOW STEP WISE THE INSIDE DETAILS AND WORKING OF THIS SCRIPT. PLEASE HELP. URGENT !!!
Please bear up with me as I don't know Python..
*Example: examples/automodel/model-full.pyhttp://salilab.org/modeller/9.11/examples/automodel/model-full.py *
# A sample script for fully automated comparative modeling from modeller import * from modeller.automodel import * # Load the automodel class
log.verbose() env = environ()
# directories for input atom files env.io.atom_files_directory = ['.', '../atom_files']
a = automodel(env, # file with template codes and target sequence alnfile = 'alignment.seg', # PDB codes of the templates knowns = ('5fd1', '1fdn', '1fxd', '1iqz'), # code of the target sequence = '1fdx') a.auto_align() # get an automatic alignment a.make() # do homology modeling
On 05/21/2013 01:45 AM, Priya Chaudhary wrote: > Using automodel model-full python script, > > 1. Do we get any changes in side chain conformations or coordinates if > the query sequence is perfectly aligned with template sequence at > sequence level. Because upon point mutations, there is no change in > sequence alignment. Whole query sequence is perfectly aligned with template.
Sure. All atoms are free to move. But with near perfect sequence identity they're going to be strongly restrained to be near the template.
> I calculated no. of contacts of wild type residues and mutant residues, > there is no change at all. I used only distance between C-alpha > atoms(CA) while calculating .
Obviously you won't see sidechain differences if you only look at C-alphas.
> 2. Can I get to know the details of a.make() and a.auto_align() commands > used in this script. I WANT TO KNOW STEP WISE THE INSIDE DETAILS AND > WORKING OF THIS SCRIPT. PLEASE HELP. URGENT !!!
I suggest you read the manual. It describes the procedure in a fair amount of detail (and also links to the 1993 JMB paper if you want more).
> Please bear up with me as I don't know Python..
If you want to know the "inside details" of a Python script, you will have to learn Python. There is a good tutorial at www.python.org.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Priya Chaudhary