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
On Jul 24, 2023, at 10:32 AM, Protya, Satirtha via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Everyone,
Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. I am facing a new issue. In one of my peptide PDB file, I need to change the Aspartate Amino Acid with Iso Aspartate Amino Acid. I have been trying to do so, but not sure how to do that. Is there any way or package that can do that?
Please let me know. Hope to hear from you soon. Have a great day.
--
Yours sincerely
Satirtha Saha
He/Him/His
Beloit College | Class of 2025
Triple Major | Biochemistry, Cognitive Science and Data Analytics
Research Assistant | Sweedler Lab | UIUC
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Funding Board Member | Beloit Student Government (BSG)
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