Hi, Can the size of geometric objects be changed? For example, can I make the ellipsoid drawn by command "measure inertia #0:167-285.A" smaller? Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031
Hi Reza, Well, the one you get from "measure inertia" is meant to show the dimensions of the the principal axes, so you couldn't get a smaller one from that command unless you used different/fewer atoms. There is no command to shrink it after you make it. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia> However, you can draw an ellipsoid surface of whatever size you want with "shape ellipsoid", see command options: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#ellipsoid> Each of the commands above is mentioned in the "see also" of the other, since they are the ways to draw an ellipsoid. Geometric objects can also be defined in BILD format and a few other ways, but they do not include ellipsoids. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#objects> 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 17, 2022, at 2:07 PM, Reza Khayat via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, Can the size of geometric objects be changed? For example, can I make the ellipsoid drawn by command "measure inertia #0:167-285.A" smaller? Thanks. Best wishes, Reza
Oops, I stand corrected! Somebody reminded me that there is a "sop transform" command with a "scale" option that you could use to shrink the ellipsoid after it was created: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html#transform> Example Chimera commands: open 2gbp measure inertia protein sop transform #1 scale 0.5 Sorry about that -- Elaine P.S. if you want to try ChimeraX, it also has all 3 commands "measure inertia" "shape ellipsoid" and "surface transform" (the latter instead of Chimera's "sop transform")
On Aug 17, 2022, at 3:09 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Reza, Well, the one you get from "measure inertia" is meant to show the dimensions of the the principal axes, so you couldn't get a smaller one from that command unless you used different/fewer atoms. There is no command to shrink it after you make it. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia>
However, you can draw an ellipsoid surface of whatever size you want with "shape ellipsoid", see command options: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#ellipsoid>
Each of the commands above is mentioned in the "see also" of the other, since they are the ways to draw an ellipsoid. Geometric objects can also be defined in BILD format and a few other ways, but they do not include ellipsoids. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#objects>
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 17, 2022, at 2:07 PM, Reza Khayat via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, Can the size of geometric objects be changed? For example, can I make the ellipsoid drawn by command "measure inertia #0:167-285.A" smaller? Thanks. Best wishes, Reza
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, Thank you and the person who reminded you! :0) Best wishes Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, August 17, 2022 7:54 PM To: Reza Khayat Cc: Chimera Subject: [EXTERNAL] Re: [Chimera-users] Geometric objects Oops, I stand corrected! Somebody reminded me that there is a "sop transform" command with a "scale" option that you could use to shrink the ellipsoid after it was created: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_sop.html-23transform&d=DwIFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ToWtLY1J0xJ1xtFCXEmAxc6Zo3Z_vroHKS3Y_hWKo72H6kJbEVk5K_hOmXvypDcc&s=sTrf_cYPJHMKJtfd5_Nz-BQg6GmUo5z_AhnhijE8JRo&e= > Example Chimera commands: open 2gbp measure inertia protein sop transform #1 scale 0.5 Sorry about that -- Elaine P.S. if you want to try ChimeraX, it also has all 3 commands "measure inertia" "shape ellipsoid" and "surface transform" (the latter instead of Chimera's "sop transform")
On Aug 17, 2022, at 3:09 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Reza, Well, the one you get from "measure inertia" is meant to show the dimensions of the the principal axes, so you couldn't get a smaller one from that command unless you used different/fewer atoms. There is no command to shrink it after you make it. <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_measure.html-23inertia&d=DwIFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ToWtLY1J0xJ1xtFCXEmAxc6Zo3Z_vroHKS3Y_hWKo72H6kJbEVk5K_hOmXvypDcc&s=oiAZqzWiWmtAW0hRp2Rn8lOYTQWsWxAoaHJcyFqV0C4&e= >
However, you can draw an ellipsoid surface of whatever size you want with "shape ellipsoid", see command options: <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_shape.html-23ellipsoid&d=DwIFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ToWtLY1J0xJ1xtFCXEmAxc6Zo3Z_vroHKS3Y_hWKo72H6kJbEVk5K_hOmXvypDcc&s=IRiD6jK3-73y3WO58plB61oZDrCdWa1h6JCCd7sItak&e= >
Each of the commands above is mentioned in the "see also" of the other, since they are the ways to draw an ellipsoid. Geometric objects can also be defined in BILD format and a few other ways, but they do not include ellipsoids. <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_print.html-23objects&d=DwIFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ToWtLY1J0xJ1xtFCXEmAxc6Zo3Z_vroHKS3Y_hWKo72H6kJbEVk5K_hOmXvypDcc&s=lHenue0H6jCB5Ar0bM9QS7YKvyscVKH6LgVoc5oCUGc&e= >
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 17, 2022, at 2:07 PM, Reza Khayat via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi, Can the size of geometric objects be changed? For example, can I make the ellipsoid drawn by command "measure inertia #0:167-285.A" smaller? Thanks. Best wishes, Reza
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_mailman_listinfo_chimera-2Dusers&d=DwIFAg&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=ToWtLY1J0xJ1xtFCXEmAxc6Zo3Z_vroHKS3Y_hWKo72H6kJbEVk5K_hOmXvypDcc&s=WIwumWjkHpmdwFipRrmWR0yPJFnVK1BaZc3bstayC8c&e=
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