Converting a carbonyl group to carboxylic acid group
Hi Elaine, I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Hi Prathvi, "before extracting" doesn't really make sense, but yes, you can do it in multiple steps: (1) delete all the atoms you don't want, i.e. everything except the serine and the carbonyl of the residue before the serine. For example, you could select the atoms you want to keep, then invert selection, then delete selection. There are lots of other ways, just use whichever you think is the easiest. (2) build the other oxygen onto the carbonyl with Build Structure (in menu under Tools... Structure Editing), Modify Structure section. That itself takes multiple steps, you would need to change the carbonyl carbon to "trigonal with 3 bonds" (keeping element C), which will put a H where you want the OH, and then you have to change that H to "O with 1 bond". You can do all this with either Chimera or ChimeraX. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h...> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 3, 2024, at 9:28 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting?
Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Hi Elaine, Thank you for your prompt response. I followed exactly the same steps as you described. Everything went fine but how to add a H-atom to the O-atom which was added at the very end? I tried the "addh" command but didn't do anything. On Mon, Jun 3, 2024 at 11:35 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Prathvi,
"before extracting" doesn't really make sense, but yes, you can do it in multiple steps:
(1) delete all the atoms you don't want, i.e. everything except the serine and the carbonyl of the residue before the serine.
For example, you could select the atoms you want to keep, then invert selection, then delete selection. There are lots of other ways, just use whichever you think is the easiest.
(2) build the other oxygen onto the carbonyl with Build Structure (in menu under Tools... Structure Editing), Modify Structure section. That itself takes multiple steps, you would need to change the carbonyl carbon to "trigonal with 3 bonds" (keeping element C), which will put a H where you want the OH, and then you have to change that H to "O with 1 bond".
You can do all this with either Chimera or ChimeraX. < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h...
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 3, 2024, at 9:28 AM, Prathvi Singh via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting?
Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
Hi Prathvi, Sorry, I think I described it wrong: to get the additional H you would need to instead choose "O with 2 bonds" in step 2 below of my instructions. Makes sense, right? that O would need 2 bonds if you want a H on it. You don't need to email both chimerax-users and chimera-users with each question. Just pick the one you are using. I hope this helps, Elaine
On Jun 6, 2024, at 8:21 AM, Prathvi Singh via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for your prompt response. I followed exactly the same steps as you described. Everything went fine but how to add a H-atom to the O-atom which was added at the very end? I tried the "addh" command but didn't do anything.
On Mon, Jun 3, 2024 at 11:35 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Prathvi,
"before extracting" doesn't really make sense, but yes, you can do it in multiple steps:
(1) delete all the atoms you don't want, i.e. everything except the serine and the carbonyl of the residue before the serine.
For example, you could select the atoms you want to keep, then invert selection, then delete selection. There are lots of other ways, just use whichever you think is the easiest.
(2) build the other oxygen onto the carbonyl with Build Structure (in menu under Tools... Structure Editing), Modify Structure section. That itself takes multiple steps, you would need to change the carbonyl carbon to "trigonal with 3 bonds" (keeping element C), which will put a H where you want the OH, and then you have to change that H to "O with 1 bond".
You can do all this with either Chimera or ChimeraX. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h...> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 3, 2024, at 9:28 AM, Prathvi Singh via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting?
Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Yes I get it now thanks a lot!!! I accidentally chose "Reply all" instead of "Reply" while replying. Will be more careful next time. Thank you so much once again On Thu, Jun 6, 2024 at 9:12 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Prathvi, Sorry, I think I described it wrong: to get the additional H you would need to instead choose "O with 2 bonds" in step 2 below of my instructions. Makes sense, right? that O would need 2 bonds if you want a H on it.
You don't need to email both chimerax-users and chimera-users with each question. Just pick the one you are using.
I hope this helps, Elaine
On Jun 6, 2024, at 8:21 AM, Prathvi Singh via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
Thank you for your prompt response. I followed exactly the same steps as you described. Everything went fine but how to add a H-atom to the O-atom which was added at the very end? I tried the "addh" command but didn't do anything.
On Mon, Jun 3, 2024 at 11:35 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Prathvi,
"before extracting" doesn't really make sense, but yes, you can do it in multiple steps:
(1) delete all the atoms you don't want, i.e. everything except the serine and the carbonyl of the residue before the serine.
For example, you could select the atoms you want to keep, then invert selection, then delete selection. There are lots of other ways, just use whichever you think is the easiest.
(2) build the other oxygen onto the carbonyl with Build Structure (in menu under Tools... Structure Editing), Modify Structure section. That itself takes multiple steps, you would need to change the carbonyl carbon to "trigonal with 3 bonds" (keeping element C), which will put a H where you want the OH, and then you have to change that H to "O with 1 bond".
You can do all this with either Chimera or ChimeraX. < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.h...
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 3, 2024, at 9:28 AM, Prathvi Singh via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting?
Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
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