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 <[log in to unmask]
> <mailto:[log in to unmask]>> 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).
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