Stuck in adding residue in the C-terminal of a segment
Dear Experts, This is regarding adding an ALA residue in the C-terminal of a specific protein domain, with CHIMERA. I have a protein-complex with multiple domains and chains. I want to add an ALA residue (101-th position) in the chain D, after the 100th residue which is PRO. I followed the tutorial and have given the following command in command line: addaa ala,101 :100.d The following outcome was: Couldn’t find ‘O’ backbone atom of PRO 100.D. Request you to kindly let me know what the possible solution could be, so that I add an ALA residue in the C-terminal of Chain D. Thank you in advance, Regards, Prathit Chatterjee
Dear Experts, This is regarding adding an ALA residue in the C-terminal of a specific protein domain, with CHIMERA. I have a protein-complex with multiple domains and chains. I want to add an ALA residue (101-th position) in the chain D, after the 100th residue which is PRO. I followed the tutorial and have given the following command in command line: *addaa ala,101 :100.d* The following outcome was: Couldn’t find ‘O’ backbone atom of PRO 100.D. Request you to kindly let me know what the possible solution could be, so that I add an ALA residue in the C-terminal of Chain D. Thank you in advance, Regards, Prathit Chatterjee On Mon, Jun 28, 2021 at 4:48 PM Prathit Chatterjee < prathit.biophysics@gmail.com> wrote:
Dear Experts,
This is regarding adding an ALA residue in the C-terminal of a specific protein domain, with CHIMERA.
I have a protein-complex with multiple domains and chains. I want to add an ALA residue (101-th position) in the chain D, after the 100th residue which is PRO.
I followed the tutorial and have given the following command in command line:
*addaa ala,101 :100.d*
The following outcome was: Couldn’t find ‘O’ backbone atom of PRO 100.D.
Request you to kindly let me know what the possible solution could be, so that I add an ALA residue in the C-terminal of Chain D.
Thank you in advance, Regards, Prathit Chatterjee
Dear Prathit Chatterjee, As the message says, proline 100 is lacking its backbone carbonyl O atom. So you can't add a residue 101 unless you complete residue 100 first. Hide ribbons and display atoms so you can see what you are doing, for example, commands something like: ~ribbon display @n,ca,c,o disp :pro focus :98-100.D (1) Select the carbonyl C atom of the proline (Ctrl-click) and use Build Structure (in menu under Tools.. Structure Editing). In that dialog use the top menu to change from Start Structure to Modify Structure, choose element C, bonds 3, geometry trigonal (because the carbonyl C is sp2-hybridized), Apply. That will add 2 hydrogens to the C. Next select one of those hydrogens, choose element O, bonds 1, set atom name to O, Apply. Now you have completed proline by adding the carbonyl O (plus an extra H that you can ignore). (2) Now you can use "addaa" to put the alanine after it. If step #1 is too hard for you, another possibility is simply to delete the partial proline and then use "addaa" two times, first to add the complete proline and then to add the alanine. 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 28, 2021, at 12:48 AM, Prathit Chatterjee via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Experts,
This is regarding adding an ALA residue in the C-terminal of a specific protein domain, with CHIMERA.
I have a protein-complex with multiple domains and chains. I want to add an ALA residue (101-th position) in the chain D, after the 100th residue which is PRO.
I followed the tutorial and have given the following command in command line:
addaa ala,101 :100.d
The following outcome was: Couldn’t find ‘O’ backbone atom of PRO 100.D.
Request you to kindly let me know what the possible solution could be, so that I add an ALA residue in the C-terminal of Chain D.
Thank you in advance, Regards, Prathit Chatterjee t: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Jun 28, 2021, at 11:01 AM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Prathit Chatterjee, As the message says, proline 100 is lacking its backbone carbonyl O atom. So you can't add a residue 101 unless you complete residue 100 first.
Hide ribbons and display atoms so you can see what you are doing, for example, commands something like:
~ribbon display @n,ca,c,o disp :pro focus :98-100.D
(1) Select the carbonyl C atom of the proline (Ctrl-click) and use Build Structure (in menu under Tools.. Structure Editing). In that dialog use the top menu to change from Start Structure to Modify Structure, choose element C, bonds 3, geometry trigonal (because the carbonyl C is sp2-hybridized),
one addition: also choose the option to leave the residue name unchanged
Apply. That will add 2 hydrogens to the C. Next select one of those hydrogens, choose element O, bonds 1, set atom name to O, Apply. Now you have completed proline by adding the carbonyl O (plus an extra H that you can ignore).
(2) Now you can use "addaa" to put the alanine after it.
If step #1 is too hard for you, another possibility is simply to delete the partial proline and then use "addaa" two times, first to add the complete proline and then to add the alanine.
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 28, 2021, at 12:48 AM, Prathit Chatterjee via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Experts,
This is regarding adding an ALA residue in the C-terminal of a specific protein domain, with CHIMERA.
I have a protein-complex with multiple domains and chains. I want to add an ALA residue (101-th position) in the chain D, after the 100th residue which is PRO.
I followed the tutorial and have given the following command in command line:
addaa ala,101 :100.d
The following outcome was: Couldn’t find ‘O’ backbone atom of PRO 100.D.
Request you to kindly let me know what the possible solution could be, so that I add an ALA residue in the C-terminal of Chain D.
Thank you in advance, Regards, Prathit Chatterjee t: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Dr. Meng, Thank you for your suggestion. I took the second suggestion and it worked. The first one was seeming a bit non-trivial because the PRO already had a C=O group in the C-terminal, but was not recognizable by Chimera, possibly because of different atomtype names (kindly see attached the snapshot). Thank you anyways, Sincerely, Prathit On Tue, Jun 29, 2021 at 3:15 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
On Jun 28, 2021, at 11:01 AM, Elaine Meng via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Prathit Chatterjee, As the message says, proline 100 is lacking its backbone carbonyl O atom. So you can't add a residue 101 unless you complete residue 100 first.
Hide ribbons and display atoms so you can see what you are doing, for example, commands something like:
~ribbon display @n,ca,c,o disp :pro focus :98-100.D
(1) Select the carbonyl C atom of the proline (Ctrl-click) and use Build Structure (in menu under Tools.. Structure Editing). In that dialog use the top menu to change from Start Structure to Modify Structure, choose element C, bonds 3, geometry trigonal (because the carbonyl C is sp2-hybridized),
one addition: also choose the option to leave the residue name unchanged
Apply. That will add 2 hydrogens to the C. Next select one of those hydrogens, choose element O, bonds 1, set atom name to O, Apply. Now you have completed proline by adding the carbonyl O (plus an extra H that you can ignore).
(2) Now you can use "addaa" to put the alanine after it.
If step #1 is too hard for you, another possibility is simply to delete the partial proline and then use "addaa" two times, first to add the complete proline and then to add the alanine.
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 28, 2021, at 12:48 AM, Prathit Chatterjee via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Experts,
This is regarding adding an ALA residue in the C-terminal of a specific protein domain, with CHIMERA.
I have a protein-complex with multiple domains and chains. I want to add an ALA residue (101-th position) in the chain D, after the 100th residue which is PRO.
I followed the tutorial and have given the following command in command line:
addaa ala,101 :100.d
The following outcome was: Couldn’t find ‘O’ backbone atom of PRO 100.D.
Request you to kindly let me know what the possible solution could be, so that I add an ALA residue in the C-terminal of Chain D.
Thank you in advance, Regards, Prathit Chatterjee t: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Prathit Chatterjee