[modeller_usage] Using only partial information for the model
To:
Subject: [modeller_usage] Using only partial information for the model
From: Stéphane Téletchéa <>
Date: Thu, 28 Feb 2008 16:49:39 +0100
Organization: INRA
Dear colleagues,
I'm willing to use modeller in a specific modelling procedure where only
specific parts of the model are wanted.
In fact, i have two beta sheets and two helices in the pdb template, and
there are linked via loops.
I would like to know the procedure i need to follow in order to model
only those subparts of the system (and use modloop for the linking part).
For instance this will be for the alignment:
>template;
structureX:18:A 63:A :::
XYZXYZ-----AAAAALLL----BBBBBLLL---AAAAALLLLL--BBBBBLLL-------*
>target;
sequence:1:::::
------CCCCCAAAAA---CCCCBBBBB---CCCAAAAA-----CCBBBBB---CCCCCCC*
The matching sections are 'A' (alpha) and 'B' (beta), other letters
being for illustration.
The template pdb contains all the coordinates for the important
structures, but not for loop LLLLL (third one).
Do i need to adjust the alignment or the python script (or both)?
I've searched through the archives and tutorials without clue, i'm
probably not getting all the process properly.
Thanks a lot in advance,
Stéphane
--
Stéphane Téletchéa, PhD. http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901