Secondary structure editing of molecules
Good morning! I have doubts about how to turn the peptide structures of the four images below (A), (B), (C), and (D) into a cartoon model like figure (E). I've tried, but I'm not succeeding. Thank you very much. -- ---- É obrigatória a utilização do e-mail @unifesp em todas as correspondências oficiais, institucionais e no acesso aos equipamentos e sistemas da Universidade Federal de São Paulo, conforme a portaria Reitoria n. 1182/2022 <https://sti.unifesp.br/documentos/termos-de-uso-do-email> que define a Política de e-mail institucional da Unifesp. <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=publicacao_visualizar&id_documento=1160855&id_orgao_publicacao=0>
Hi Gabrielle, Just hide atoms and show ribbon. However, if there is no helix or strand in that part, it will just be a thin string like the red part in "E". Also it must be a peptide or nucleotide chain. If it is not recognized as either of those, there will not be any ribbon. There are lots of ways to hide atoms and show ribbon, but here are example commands: ~display ribbon Maybe your structure does not have helix or strand. If you want to force Chimera to think some residues are helix or strand you can select them, then use Selection Inspector (click green magnifying glass on bottom right corner to open that), then in that dialog, inspect: Residues, and change the "in helix" and "in strand" settings for the selected residues. How to select: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> Selection Inspector help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.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 Aug 8, 2023, at 4:29 AM, GABRIELLE LUPETI DE CENA via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Good morning! I have doubts about how to turn the peptide structures of the four images below (A), (B), (C), and (D) into a cartoon model like figure (E). I've tried, but I'm not succeeding. Thank you very much.
Thank you very much! It helped a lot, I achieved what I wanted. Em ter., 8 de ago. de 2023 às 13:18, Elaine Meng <meng@cgl.ucsf.edu> escreveu:
Hi Gabrielle, Just hide atoms and show ribbon. However, if there is no helix or strand in that part, it will just be a thin string like the red part in "E". Also it must be a peptide or nucleotide chain. If it is not recognized as either of those, there will not be any ribbon.
There are lots of ways to hide atoms and show ribbon, but here are example commands:
~display ribbon
Maybe your structure does not have helix or strand. If you want to force Chimera to think some residues are helix or strand you can select them, then use Selection Inspector (click green magnifying glass on bottom right corner to open that), then in that dialog, inspect: Residues, and change the "in helix" and "in strand" settings for the selected residues.
How to select: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
Selection Inspector help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.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 Aug 8, 2023, at 4:29 AM, GABRIELLE LUPETI DE CENA via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Good morning! I have doubts about how to turn the peptide structures of the four images below (A), (B), (C), and (D) into a cartoon model like figure (E). I've tried, but I'm not succeeding. Thank you very much.
-- ---- É obrigatória a utilização do e-mail @unifesp em todas as correspondências oficiais, institucionais e no acesso aos equipamentos e sistemas da Universidade Federal de São Paulo, conforme a portaria Reitoria n. 1182/2022 <https://sti.unifesp.br/documentos/termos-de-uso-do-email> que define a Política de e-mail institucional da Unifesp. <https://sei.unifesp.br/sei/publicacoes/controlador_publicacoes.php?acao=publicacao_visualizar&id_documento=1160855&id_orgao_publicacao=0>
participants (2)
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Elaine Meng -
GABRIELLE LUPETI DE CENA