Hi Dorota,
On 12/02/2020 16:40, Dorota Kubacka wrote:
I would like to mutate one aa into non standard residue, namely GLU with ribose
covalently linked.
I already have mol file of the new structure (GLU+ribose), I've generated pdb
and cif files in PRODRG program, changed the type of molecule to ' L-peptide in
cif file.
But I don't know what should I do with pdb and cif file to could use command in
coot GUI:
Extensions -> Modelling -> Replace Residue...
You need to read in the cif file for your modified aa. Then use Replace Residue. Then you will have to drag
around the ribose to fit the density.
But.........
>
> I would like to mutate one aa into non standard residue,
As Takanori might say, "you do not want to mutate one aa into a non-standard
one"
:-) Haha I couldn't resist (the in-joke(?) for CCPEM readers).
> namely GLU with ribose covalently linked.
If I may be so bold, this is the wrong approach (WA) - let's call the other approach the Acedrg-Link Method
(ALM).
> I already have mol file of the new structure (GLU+ribose),
Yes, you would need that for the WA, but not for the ALM
> I've generated pdb and cif files in PRODRG program,
The CCP4 program for dictionary generation is Acedrg these days. How did you
hear about PRODRG?
> changed the type of molecule to ' L-peptide in cif file.
:-) Cunning.
But... now to my point: what I think you want to do is create a LINK between the GLU and the ribose rather
than create a modified GLU. Acedrg can make the link dictionary for you now. I believe that there is a
GUI in CCP4i2 under Ligands presumably - and there is one in Coot too, it's in the CCP4 Modules menu and
creates a new menu item.
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/acedrg-link-usage-notes.txt
I will try to make a video for this sort of thing, it's becoming a FAQ.
Paul.
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