Regarding replacing Aspartate with Isoaspartate
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 Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_medium=referral> sahass@beloit.edu<mailto:sahass@beloit.edu> [Image][Image]
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 Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615 <tel:+16084736615> Schedule an Appointment <https://admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_medium=referral> sahass@beloit.edu <mailto:sahass@beloit.edu> <image001.png><image002.png> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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. * Satirtha 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 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 Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://urldefense.com/v3/__https:/admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_medium=referral__;!!DZ3fjg!_286KnLDhuD5crdU4SQPw3nfCD6hRRDwX6eyAkmO0fy7yF6tXjOt2o57gYJf18XOH4OfpEhQpSCW0LICL6FB$> sahass@beloit.edu<mailto:sahass@beloit.edu> <image001.png><image002.png> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/<https://urldefense.com/v3/__https:/mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/__;!!DZ3fjg!_286KnLDhuD5crdU4SQPw3nfCD6hRRDwX6eyAkmO0fy7yF6tXjOt2o57gYJf18XOH4OfpEhQpSCW0Mb1N4f8$>
participants (2)
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Eric Pettersen -
Protya, Satirtha