[Chimera-users] use of the program UCSF Chimera

GABRIELLE LUPETI DE CENA gabrielle.lupeti at unifesp.br
Thu May 12 06:30:09 PDT 2022

Hello Elaine, Thank you very much for your attention!

I managed to solve the problem ♥

Em seg., 9 de mai. de 2022 às 21:26, Elaine Meng <meng at cgl.ucsf.edu>

> Hello Gabrielle,
> Just hide the atoms and show the ribbon.  For example, menu:
> Actions... Atoms/Bonds... hide
> Actions... Ribbons... show
> Or, if you want to use commands instead of the menu:
> ~display
> ribbon
> See command help:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
> To learn Chimera, you might be interested in trying some of the tutorials:
> <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
> <https://www.rbvi.ucsf.edu/chimera/tutorials.html>
> If you mean that when you first open the structure it looks different, it
> might be because there are different numbers of atoms, and that is one of
> the ways Chimera tries to guess which type of display might be most
> useful.  But if you don't want the style you get, you can just change it
> with the menu or commands as explained above.
> If you really need it to look that way right when you open it, without
> changing it yourself, use Preferences (menu: Favorites... Preferences),
> category "New Molecules" -- there you can set "smart initial display" (the
> guessing stuff) to "false" and "ribbon display" to "on" and "show atoms" to
> "false"; you would probably also want atom style "endcap" and bond style
> "stick" in case you decide to show some atoms later.  If you want to keep
> these settings for the next time you use Chimera, remember to click Save on
> the Preferences dialog.
> New Molecules Preferences:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules
> >
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On May 9, 2022, at 5:09 PM, GABRIELLE LUPETI DE CENA via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Goodnight!
> >
> > My name is Gabrielle, I am a Master's student at UNIFESP (Federal
> University of São Paulo), SP, Brazil.
> > I'm using UCSF Chimera to analyze the secondary structure of some
> peptides that I'm studying.
> >
> > When I load the .pdb file in the program, it generates a different
> structure than the one desired. In the examples below, we have two
> structures alpha helix and random coil, but the images generated are
> different and I don't understand why.
> >
> > Could you help me, explaining what is happening, or what I should do to
> have the image as in the first figure (NATTP_05 chimera).
> > Thanks

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