Re: [Chimera-users] How to show hydrophobility clearly
Hi Kenji In this latest message, you are using one method that shows the pocket surface only, like in the tutorial. Your image after step 1 of what you tried looks OK to me: But if you are not happy with that, I am guessing you do not want this method. If you want it to look more like this example image with the labeling "hydrophobic pocket" and "allosteric tunnel" ...then you need to use a DIFFERENT method that includes clipping: showing the whole surface of the protein and then using clipping to slice. We already discussed this method, and you were already using this method the first time you asked the question: <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018741.html> <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018746.html> With that method, all you can do is to move and rotate the structure and move the clipping (either global clipping plane with Side View tool or surface-only clipping with Per-Model Clipping, both mentioned in previous replies) to try to get a good view. However, different pockets are different shapes and depending on the shape of your pocket it may not be possible to make an image that clearly shows what you want. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 26, 2022, at 6:40 PM, Kenji MATSUI <s214903z@st.go.tuat.ac.jp> wrote:
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 am looking at ligand-protein interactions and how they affect binding affinity.
Therefore, I would like to examine the hydrophobicity and hydrophilicity around the ligand in the figure(third)
If you know of any, could you please let us know?
I tried to show what you mentioned in your email.(clip off, mclip)
I apologize for asking this question so often in your busy schedule, but I would appreciate it if you could confirm it for me.
<image.png> <image.png>
The picture I want to show <image.png>
Tried thing 1. clip off +~ribbon <1edf41f0-9f2e-4921-92fe-19399979fd97.png>
2.m clip <image1.png>
. ---------------------------------------------------------------------------
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 <Hydrohobility_1P8D_LXR_LBD_mono_24,25-epoxycholesterol.pyc>
Dear Elaine Thank you for your reply. I now know that I have to try it the way you taught me before. I will try to adjust it again. Thank you very much for your kind replies. --------------------------------------------------------------------------- 松井 健治 東京農工大学大学院 工学府産業技術専攻 修士 2年 〒184-8588 東京都小金井市中町2-24-16 Mail: s214903z@st.go.tuat.ac.jp 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7月28日(木) 0:46 Elaine Meng <meng@cgl.ucsf.edu>:
Hi Kenji In this latest message, you are using one method that shows the pocket surface only, like in the tutorial. Your image after step 1 of what you tried looks OK to me: [image: 1edf41f0-9f2e-4921-92fe-19399979fd97.png] But if you are not happy with that, I am guessing you do not want this method.
If you want it to look more like this example image with the labeling "hydrophobic pocket" and "allosteric tunnel"
...then you need to use a DIFFERENT method that includes clipping: showing the whole surface of the protein and then using clipping to slice.
We already discussed this method, and you were already using this method the first time you asked the question: <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018741.html> <https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-July/018746.html>
With that method, all you can do is to move and rotate the structure and move the clipping (either global clipping plane with Side View tool or surface-only clipping with Per-Model Clipping, both mentioned in previous replies) to try to get a good view. However, different pockets are different shapes and depending on the shape of your pocket it may not be possible to make an image that clearly shows what you want.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 26, 2022, at 6:40 PM, Kenji MATSUI <s214903z@st.go.tuat.ac.jp> wrote:
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 am looking at ligand-protein interactions and how they affect binding affinity.
Therefore, I would like to examine the hydrophobicity and hydrophilicity around the ligand in the figure(third)
If you know of any, could you please let us know?
I tried to show what you mentioned in your email.(clip off, mclip)
I apologize for asking this question so often in your busy schedule, but I would appreciate it if you could confirm it for me.
<image.png> <image.png>
The picture I want to show <image.png>
Tried thing 1. clip off +~ribbon <1edf41f0-9f2e-4921-92fe-19399979fd97.png>
2.m clip <image1.png>
. ---------------------------------------------------------------------------
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 <Hydrohobility_1P8D_LXR_LBD_mono_24,25-epoxycholesterol.pyc>
participants (2)
-
Elaine Meng -
Kenji MATSUI