-------- Original Message --------
Subject: Re: question related to peptide baton build
Date: Mon, 21 Nov 2011 16:47:43 +0000
From: Paul Emsley <[email protected]>
To: Dialing Pretty <[email protected]>, "[email protected]"
<[email protected]>
On 19/11/11 06:39, Dialing Pretty wrote:
Dear All,
I am using baton to build a peptide.
Coot's CA->Mainchain tool doesn't work for less than 6 residues (hhmm...
maybe does 5, not sure...).
I use the Validate-unmodelled blobs 2Fo-Fc map got the green blob (the
green blob is about 7 residues long). Then I use the Calculate-other
modelling tools-Calpha Baton mode to get the yellow skeleton.
Very good...
I find the yellow scheleton is much longer than the green blobs at
both ends of the green blob (At each end of the green blob the yellow
skeleton is about 1-2 residues longer).
This can happen...
Coot has a guess at the lower limit for skeletons, it may get it wrong...
In this situation I only build the pepttide for the length of the
green blob or I build the peptide for the length of yellow skeleton?
Only the parts that you think are real.
You can change the contour parameters with Edit -> Skeletonization
Parameters.
In some situation I find the green blob was divided into 2 parts, one
part is about 5-6 residues, one part is about 2 residues, between the
2 parts there is space of about 1-2 residues without green blob. In
this situation how can I process the peptide baton build?
Sometimes you need to take a leap of faith.
(I mean by that, you sometimes need to place a CA where there is little
or no density).
Paul.
