Dear Modellers, I have a pretty small question. Is there a way in MODELLER where i can completely use a single template along with its side-chain topology? So while aligned with target, I would expect that the template's backbone and side-chain relative orientations, topology and architecture is properly copied from the considered template, and then I would expect MODELLER to model the unaligned flexible chunks through the exactly copied scaffolds from the template.
In normal modelling scripts, it simply harness the peptide backbone localization information from the template and then fixes the side-chains with its own algorithms.
HOW CAN I GET MY QUERY SOLVED WITH AN ADDITIONAL LINE IN MODEL-SINGLE.PY TO COMPLETELY EMPLOY TEMPLATE WITH ITS PEPTIDE BACKBONE ALONG WITH SIDE-CHAINS?
Thanks Ashish
Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA
On 04/22/2012 02:17 AM, Ashish Runthala wrote: > I have a pretty small question. Is there a way in MODELLER where i > can completely use a single template along with its side-chain > topology?
Where you have a 1:1 alignment, the initial model is exactly the same as the template. If you don't want Modeller to optimize this, you can override select_atoms():
http://salilab.org/modeller/9.10/manual/node23.html
> In normal modelling scripts, it simply harness the peptide backbone > localization information from the template and then fixes the > side-chains with its own algorithms.
No, the initial model is simply copied from the template where the atom names are the same (this usually means the backbone and part of the sidechain, depending on the type of the aligned residue). Side chain dihedrals are not strongly restrained though, so during optimization they can certainly move from these initial positions.
Ben Webb, Modeller Caretaker
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Ashish Runthala -
Modeller Caretaker