From: Kenji MATSUI <s214903z@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@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
Second photo
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
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@st.go.tuat.ac.jp 2022年8月24日(水) 0:16 Elaine Meng <meng@cgl.ucsf.edu>:
*From: *Kenji MATSUI <s214903z@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@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#hy...
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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Kenji MATSUI