[Chimera-users] [EXTERNAL] Re: Geometric objects

[Reza Khayat]

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 at 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 at 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 at 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
>
>
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