Hi,
I have tried to use the methods. I was successful to do so for small sequence. But for larger sequences is there any particular selection command for selecting OXT?
Hope to hear from you soon. Have a great day.
From:
Eric Pettersen <pett@cgl.ucsf.edu>
Date: Thursday, July 20, 2023 at 4:39 PM
To: Protya, Satirtha <ssprotya@illinois.edu>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Regarding Usage of ChimeraX for PDB file creation
Hi Satirtha,
ChimeraX cannot directly create D-amino acids, but it is easy to change from L- to D-. Let’s say you want to change residue 2 to D-. Just select the carbon alpha of residue
2 and use the “Invert” section of Build Structure to invert the chirality of the carbon alpha substituents. The equivalent command is “build invert :2@ca”.
To amidate the C-terminus, select the OXT connected to the terminus and use the “Modify Structure” section of Build Structure to change the OXT to nitrogen with 3 bonds and planar
geometry. Depending on what you intend to do with the modified structure you might also want to use that section to change the name of the amidated residue, or put the admidation in a residue of its own.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab