[Chimera-users] How to show hydrophobility clearly

[Elaine Meng]

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 at 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 at st.go.tuat.ac.jp
> <Hydrohobility_1P8D_LXR_LBD_mono_24,25-epoxycholesterol.pyc>

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