How to examine the hydrophobicity and hydrophilicity around the ligand
Dear Chimera
Thank you for taking the time to answer my question the other day.
I also apologize for contacting you outside of business hours due to the time difference.
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 below（second photo,）.
[image: image10.png]
[image: image.png] second photo
Methods Tried select→ligand→Focus
This method causes some parts of the surface to be difficult to see. As shown in the second photo, it is difficult to see the degree of hydrophobicity around the ligand.
[image: image.png]
Please confirm.
--------------------------------------------------------------------------- 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
Hi Kenji, There is no need to apologize for the time of the message -- no matter when you send it, I can wait to answer until I am at work.
Yes, that is a common problem with showing parts of the surface. There is no simple solution, you just have to try showing and hiding different parts of the surface. Sometimes you can rotate the structure so that the clipping (where the front is sliced off) is at a better position to show the pocket. Even if you turn off clipping, sometimes it is possible to hide the outer surface and show only the pocket, but it depends on the shape of the surface.
There is an example in the Structure Analysis and Comparison tutorial, in the "Surfaces and Attributes" section, of showing only the pocket surface around the ligand: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#surfaces
That example uses "sop zone" to show only the surface of receptor atoms within 5 angstroms of ligand; you could use some other distance if it looks better in your structure.. Again, however, whether that looks good enough depends on the shape of the surface and the pocket.
If you want to turn off the front/back clipping, you can use command "clip off". Another thing you can try (but that would also take time to experiment) is Per-Model Clipping tool, where you can turn on a clipping plane, but then rotate it by hand to any angle. You can make the clipping plane only affect the surface and not the atoms. https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html
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 20, 2022, at 12:17 AM, Kenji MATSUI via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Chimera
Thank you for taking the time to answer my question the other day.
I also apologize for contacting you outside of business hours due to the time difference.
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 below（second photo,）.
<image10.png>
<image.png> second photo
Methods Tried select→ligand→Focus
This method causes some parts of the surface to be difficult to see. As shown in the second photo, it is difficult to see the degree of hydrophobicity around the ligand.
<image.png>
Please confirm.
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
Dear Elaine
Thank you for taking the time to reply.
Based on the method you taught me, I have displayed it as shown in the figure below.
*Command*: *~ribbon https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbon.html*
[image: image3.png]
I am very sorry,
I'm thinking of cropping out half of this surface because I want to show the surface clearly, but what should I do to have the diagram output as described in the paper for the second photo?
[image: image.png]
What I did.
I went through the tutorial on Chimera. I tried to display it in clip, but it did not work --------------------------------------------------------------------------- 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
2022年7月20日(水) 23:59 Elaine Meng meng@cgl.ucsf.edu:
Hi Kenji, There is no need to apologize for the time of the message -- no matter when you send it, I can wait to answer until I am at work.
Yes, that is a common problem with showing parts of the surface. There is no simple solution, you just have to try showing and hiding different parts of the surface. Sometimes you can rotate the structure so that the clipping (where the front is sliced off) is at a better position to show the pocket. Even if you turn off clipping, sometimes it is possible to hide the outer surface and show only the pocket, but it depends on the shape of the surface.
There is an example in the Structure Analysis and Comparison tutorial, in the "Surfaces and Attributes" section, of showing only the pocket surface around the ligand: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html
< https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#su...
That example uses "sop zone" to show only the surface of receptor atoms within 5 angstroms of ligand; you could use some other distance if it looks better in your structure.. Again, however, whether that looks good enough depends on the shape of the surface and the pocket.
If you want to turn off the front/back clipping, you can use command "clip off". Another thing you can try (but that would also take time to experiment) is Per-Model Clipping tool, where you can turn on a clipping plane, but then rotate it by hand to any angle. You can make the clipping plane only affect the surface and not the atoms. < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-mod...
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 20, 2022, at 12:17 AM, Kenji MATSUI via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera
Thank you for taking the time to answer my question the other day.
I also apologize for contacting you outside of business hours due to the
time difference.
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 below（second photo,）.
<image10.png>
<image.png> second photo
Methods Tried select→ligand→Focus
This method causes some parts of the surface to be difficult to see. As shown in the second photo, it is difficult to see the degree of
hydrophobicity around the ligand.
<image.png>
Please confirm.
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
Hi Kenji, The shape of pocket will be different in different proteins so you can never get it to look exactly the same as some other example. Making figures is always a long trial and error for each different protein with lots of hand rotation and other interactive movements, it is not something that is solved by some expert command that I could give you. However, you can sometimes make an image similar to other images you have seen.
Your first image in your original message
...already looks similar to the second one to me
... it is just that the shape of the pocket is different -- you just have to experiment with the position of the clipping plane and the rotation of the structure to show it as best as possible. The front/back clipping can also be adjusted in the Side View tool (menu: Favorites... Side View).
If you mean that you want the dark gray color instead of the light orange, you can change that cap color using the Surface Capping tool (menu Tools... Depiction... Surface Capping), turn on "Use cap color" and then click the square color area and use the color chooser to change the color.
Another kind of clipping allows clipping only the surface but not clipping the ligand. For this, you have to use the Per-Model Clipping tool ( menu: Tools... Depiction... Per-Model Clipping) https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html ...and in that tool, choose the surface model as the model to clip, activate clipping, and then try moving the clipping plane with the mouse or trackpad. It requires some practice using it and can take a lot of time moving everything around to make it look good. Again, you might not need to use this, if you can use the simple front/back clipping that you already tried.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 20, 2022, at 7:50 PM, Kenji MATSUI via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Elaine
Thank you for taking the time to reply.
Based on the method you taught me, I have displayed it as shown in the figure below.
Command: ~ribbon
<image3.png>
I am very sorry,
I'm thinking of cropping out half of this surface because I want to show the surface clearly, but what should I do to have the diagram output as described in the paper for the second photo?
<image.png>
What I did.
I went through the tutorial on Chimera. I tried to display it in clip, but it did not work
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
2022年7月20日(水) 23:59 Elaine Meng meng@cgl.ucsf.edu: Hi Kenji, There is no need to apologize for the time of the message -- no matter when you send it, I can wait to answer until I am at work.
Yes, that is a common problem with showing parts of the surface. There is no simple solution, you just have to try showing and hiding different parts of the surface. Sometimes you can rotate the structure so that the clipping (where the front is sliced off) is at a better position to show the pocket. Even if you turn off clipping, sometimes it is possible to hide the outer surface and show only the pocket, but it depends on the shape of the surface.
There is an example in the Structure Analysis and Comparison tutorial, in the "Surfaces and Attributes" section, of showing only the pocket surface around the ligand: https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#surfaces
That example uses "sop zone" to show only the surface of receptor atoms within 5 angstroms of ligand; you could use some other distance if it looks better in your structure.. Again, however, whether that looks good enough depends on the shape of the surface and the pocket.
If you want to turn off the front/back clipping, you can use command "clip off". Another thing you can try (but that would also take time to experiment) is Per-Model Clipping tool, where you can turn on a clipping plane, but then rotate it by hand to any angle. You can make the clipping plane only affect the surface and not the atoms. https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html
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 20, 2022, at 12:17 AM, Kenji MATSUI via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Chimera
Thank you for taking the time to answer my question the other day.
I also apologize for contacting you outside of business hours due to the time difference.
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 below（second photo,）.
<image10.png>
<image.png> second photo
Methods Tried select→ligand→Focus
This method causes some parts of the surface to be difficult to see. As shown in the second photo, it is difficult to see the degree of hydrophobicity around the ligand.
<image.png>
Please confirm.
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
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participants (2)
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Elaine Meng -
Kenji MATSUI