On 07/12/11 11:58, matthew vetting wrote:
I think you are probably asking the wrong question, and what you are
eventually going to want to know is how do I get a modified amino acid
recognized in PHENIX or REFMAC so that it makes proper peptide bonds.
The making and breaking of bonds in COOT (or O for ligands) is not
something that gets utilized downstream in PHENIX or REFMAC, that is
better done in ligand construction programs.
As far as making the modified amino acid I would use
Chemdraw/Chemdraw3d then export and use PRODRG to make a cif file,
though there are many nice ligand construction tools out there today
(including one in PHENIX I believe).
Matt Vetting
On Tue, Dec 6, 2011 at 5:10 PM, Saugata Hazra <saugata_i...@yahoo.com
<mailto:saugata_i...@yahoo.com>> wrote:
Hello Everyone,
I'm sorry if its a silly question. I used to use "O" and recently
started working with "COOT". I am wondering how to make covalent
bond in coot, between a modified substrate and regular protien
residue. I can not figure out how to make the bond.
OK, so we are still playing "guess what the question should have been"?
What fun! OK then...
Yes, quite so. And in Coot [1].
Anyway, you'll need to make the group of the resulting monomer
"L-peptide" for Coot to draw the bond. And the resulting atoms should
be HETATMs of course (if you use the Coot interface that gets fixed on
the fly).
Paul.
[1] I suspect the days of chemdraw->prodrg->graphics are numbered...
(well, I can hope).
