[Chimera-users] How to display hydrohobic area

[Kenji MATSUI]

Dear Elaine

Thank you for replying to your email.

Thank you for your continued support.
---------------------------------------------------------------------------
Kenji Matsui
 Graduate School of Tokyo University of Agriculture and Technology M2
2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
 Mail: s214903z at st.go.tuat.ac.jp


2022年8月24日(水) 0:16 Elaine Meng <meng at cgl.ucsf.edu>:

>
> *From: *Kenji MATSUI <s214903z at st.go.tuat.ac.jp>
> *Subject: **How to display hydrohobic area*
> *Date: *August 22, 2022 at 9:17:37 PM PDT
> *To: *Elaine Meng <meng at cgl.ucsf.edu>
>
> Dear Chimera
> Thank you for taking the time to answer my question the other day.
> I'm Kenji Matsui, a second-year master's student at a national university
> in Japan.
>
> I would like to display the hydrophobicity of the protein around the
> ligand like the first picture, but I couldn't do it.
> How can I do this?
> When I actually did it, it turned out to be the second picture.
>
> I apologize for asking this question so often in your busy schedule, but I
> would appreciate it if you could confirm it for me.
>
> First photo
> [image: image.png]
>
> Second photo
> [image: image.png]
>
> Hi Kenji,
> If I understand correctly, you want to show the amino acid hydrophobicity
> coloring on the ribbon and sticks, not the molecular surface.
>
> When you open the structure, it may already be displayed as ribbon and
> sticks.  Do not show the surface.  (Or, if you already are showing the
> surface, you can hide it with menu: Select... Clear Selection,  menu:
> Actions... Surface... hide)  Then you can use the "rangecolor" command to
> color protein ribbons/sticks by hydrophobicity:
>
> rangecolor kdHydrophobicity min dodger blue 0 white max orange red
>
> See rangecolor help
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html>
>
> That command is part of the tutorial for surface coloring:
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#hydrophobicity
> >
>
> However, when the surface is not shown, you can see that this comand also
> colors the other representations (ribbons and sticks).
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
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