On 11/09/13 22:03, Uma Ratu wrote:
Hi, Bernhard and Yury:
I did change Cys to CSX or CSO with older version of Coot. And the
program replace the residue inner the chain.
With present Coot-0.7, it seems to be complicated to replace a residue.
Thank you for your suggestions.
Uma
On Wed, Sep 11, 2013 at 4:40 PM, Bernhard Lechtenberg
<[email protected]
<mailto:[email protected]>> wrote:
Hi Uma,
when I do the same procedure (in OSX, but the problem seems to be
the same), the new residue is stored in a new chain with residue
number 1. So you would need to renumber the residue and change the
chain ID back to the original chain ID. It's annoyingly
complicated, but it works for me.
Hope that helps,
Bernhard
On Sep 11, 2013, at 12:56 PM, Uma Ratu <[email protected]
<mailto:[email protected]>> wrote:
Hello,
I try to replace one of cysteine residue to CSX using Win-coot.
Here is how I did:
Extensions > Modelling > Replace Residue... and enter the three
letter code.
The program place the CSX residue, but with break bond. The new
residue is no longer linked with other residue and not in the chain.
I then try to replace with other residues, such as ALA. The
results are the same: the new residues all with break bond.
How could I put the replaced residue back to the main-chain?
I use Win-coot-0.7.
Thank you
Uma
What is the group of CSX? If you tell coot that it is not an "L-peptide"
(or in modern coots, simply "peptide" will do) , it will believe you
(and thus not create peptide bonds).
Edit -> Restraints -> CSX -> Info -> Group
I just tried with Coot-0.8-pre and the latest Refmac Monomer Library and
it seemed to work.
Paul.
