Hi Eric,
Thank you for your reply. I will try to use this method and let you know if I face any issue. Have a great day.
From:
Eric Pettersen <pett@cgl.ucsf.edu>
Date: Monday, July 24, 2023 at 7:26 PM
To: Protya, Satirtha <ssprotya@illinois.edu>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Regarding replacing Aspartate with Isoaspartate
Hi Satirtha,
I don’t know that there’s any great solutions, since isoaspartate needs more room for its backbone than aspartate, Here’s a crude idea of how to do it in ChimeraX. Let’s assume that your aspartate residue
is number 9 in chain A, then:
(1) Open an isoaspartate residue from the CCD: “open ccd:ias” (assume it opens in model 2)
(2) Delete the hydrogens and OD2 atom: “del #2@od2; del #2 & H”
(3) Get it very roughly positioned correctly: “align #2@od1,ca,n to #1/A:9@c,ca,n”
(4) Delete the aspartate: “del #1/A:9”
(5) Combine the models: “combine #1,2 close true”.
(6) Possibly adjust the positioning of some or all of the isoaspartate atoms with “Move atoms” right mouse mode or by control double-clicking a bond and choosing “Adjust Torsion” from the popup menu to adjust
the bond torsion angle.
(7) Make the inter-residue bonds: “bond /A:8@c #1:ias@n reasonable false ; bond /A:10@n :ias@cg reasonable false”
(8) Save the result as a PDB file
(9) Edit the PDB file and change the “ATOM “ records (ATOM + 2 spaces) to “HETATM” records.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab