Re: [modeller_usage] Urgent Query . Please do reply. Thanks a ton.
To: Priya Chaudhary <>
Subject: Re: [modeller_usage] Urgent Query . Please do reply. Thanks a ton.
From: Modeller Caretaker <>
Date: Tue, 21 May 2013 16:47:29 -0700
Cc:
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.