Silhouettes only on selected models
Hi, I'm writing to know if there is a way to turn on the silhouette graphical option only on selected models in ChimeraX, or is it just a global option? I have a model of an enzyme with its ligand and another model with the electron density loaded from a .map file. I want to display the electron density around the ligand as a slightly transparent mesh without silhouettes (see below) while still having silhouettes on the enzyme and ligand. Is there a way to do this? The silhouettes on the mesh make it too dark and dense (see image 2). Thank you very much Pedro Bule [image: image.png] [image: image.png] -- *Pedro Bule* *Assistant Professor* GLYCOBIOLOGY AND STRUCTURAL ENZYMOLOGY LAB *P:* (+351) 21 365 28 84 // 431379 | pedrobule@fmv.ulisboa.pt <email@fmv.ulisboa.pt> *Centro de Investigação Interdisciplinar em Sanidade Animal* Faculdade de Medicina Veterinária Av. Universidade Técnica | 1300-477 Lisboa | PORTUGAL
Hi Pedro, Sorry no, there is no option to put silhouettes only some model(s) and not others. It is a global setting: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes> Sometimes you can approximately "fake" this effect by using the selection outline. It is not the same, however, as silhouettes; it will only go around the outside perimeter of the selected item(s). See this previous post for an example set of commands: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/X7UN5ACWPO5ZSYU3BHLFWGTLTPWDXVHW/> See also this previous post about the poor appearance of silhouettes on mesh: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/NFNED62LWN6M3QVABBRTVSS5C2QTFN2V/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 6, 2024, at 5:47 AM, Pedro Bule via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I'm writing to know if there is a way to turn on the silhouette graphical option only on selected models in ChimeraX, or is it just a global option? I have a model of an enzyme with its ligand and another model with the electron density loaded from a .map file. I want to display the electron density around the ligand as a slightly transparent mesh without silhouettes (see below) while still having silhouettes on the enzyme and ligand. Is there a way to do this? The silhouettes on the mesh make it too dark and dense (see image 2). Thank you very much Pedro Bule
Hi Pedro, A trick to get silhouettes on just your atomic model is to add them in a photo editing program like Gimp or Photoshop. It takes a bit of work. Save your image without silhouettes, and an image without the mesh with silhouettes. Then in the photo editing program use the silhouette image and erase everything except the black and then compose that which is the silhouette lines around the atomic model with the image that does not have silhouettes. Tom
On Mar 6, 2024, at 7:36 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pedro, Sorry no, there is no option to put silhouettes only some model(s) and not others. It is a global setting: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes>
Sometimes you can approximately "fake" this effect by using the selection outline. It is not the same, however, as silhouettes; it will only go around the outside perimeter of the selected item(s). See this previous post for an example set of commands: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/X7UN5ACWPO5ZSYU3BHLFWGTLTPWDXVHW/>
See also this previous post about the poor appearance of silhouettes on mesh: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/message/NFNED62LWN6M3QVABBRTVSS5C2QTFN2V/>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 6, 2024, at 5:47 AM, Pedro Bule via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi, I'm writing to know if there is a way to turn on the silhouette graphical option only on selected models in ChimeraX, or is it just a global option? I have a model of an enzyme with its ligand and another model with the electron density loaded from a .map file. I want to display the electron density around the ligand as a slightly transparent mesh without silhouettes (see below) while still having silhouettes on the enzyme and ligand. Is there a way to do this? The silhouettes on the mesh make it too dark and dense (see image 2). Thank you very much Pedro Bule
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participants (3)
-
Elaine Meng -
Pedro Bule -
Tom Goddard