Re: [chimerax-users] [Chimera-users] How to caluculate buried surface area
Hi Kenji, You are using ChimeraX? I CC'd the ChimeraX address chimerax-users@cgl.ucsf.edu (different than chimera-users@cgl.ucsf.edu).
The "measure buriedArea" command does not require picking any blobs. You just specify the parts that you want in the command line. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
So, maybe something like command:
measure buriedarea protein with ligand
...but maybe "ligand" doesn't get your ligand. You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead:
measure buriedarea protein with :UNK
You sent a Pymol session... I don't use Pymol so I can't open that file, sorry. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Chimera
I am sorry to interrupt your busy schedule.
My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day.
We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand.
For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein.
What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time.
In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area.
I tried to check and tried , but it did not work.
1.See https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html
2.Try to use measure blob using chimera X. Reference: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
However, I didn't know how to solve this command. Command ;ui mousemode right "pick blobs
Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html
Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
<Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove LXRβ_1P8D).pse>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Dear Elane
Thank you for your time and response.
My name is Matsui, and I am a second-year master's student at a Japanese university.
I am also using ChimeraX.
But first I will try the method you showed me with chimera, and if it doesn't work, I will try it with chimeraX as well. --------------------------------------------------------------------------- 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9月6日(火) 23:30 Elaine Meng meng@cgl.ucsf.edu:
Hi Kenji, You are using ChimeraX? I CC'd the ChimeraX address chimerax-users@cgl.ucsf.edu (different than chimera-users@cgl.ucsf.edu).
The "measure buriedArea" command does not require picking any blobs. You just specify the parts that you want in the command line. < https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
So, maybe something like command:
measure buriedarea protein with ligand
...but maybe "ligand" doesn't get your ligand. You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead:
measure buriedarea protein with :UNK
You sent a Pymol session... I don't use Pymol so I can't open that file, sorry. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera
I am sorry to interrupt your busy schedule.
My name is Matsui, and I am a second-year master's student at a Japanese
university.
Thank you for taking time out of your busy schedule to respond to my
question the other day.
We are investigating the buried surface area to see the magnitude of the
interaction between protein and ligand.
For this purpose, I calculated the solvent accessible area of the
ligand. However, the value is 9955, which shows the entire surface area of the protein.
What should I do? I am not in a hurry for answers , so I would
appreciate a reply when you have the time.
In this case, the ligand was in the binding pocket of the protein, so I
would like to calculate the ligand's solvent contact area = buried surface area.
I tried to check and tried , but it did not work.
1.See
https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html
2.Try to use measure blob using chimera X. Reference:
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
However, I didn't know how to solve this command. Command ;ui mousemode right "pick blobs
Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html
Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
<Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove
LXRβ_1P8D).pse>_______________________________________________
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription:
Dear Kenji, The example commands in my previous message are for ChimeraX, not Chimera. Elaine
On Sep 7, 2022, at 7:06 AM, Kenji MATSUI via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Elane
Thank you for your time and response.
My name is Matsui, and I am a second-year master's student at a Japanese university.
I am also using ChimeraX.
But first I will try the method you showed me with chimera, and if it doesn't work, I will try it with chimeraX as well.
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9月6日(火) 23:30 Elaine Meng meng@cgl.ucsf.edu: Hi Kenji, You are using ChimeraX? I CC'd the ChimeraX address chimerax-users@cgl.ucsf.edu (different than chimera-users@cgl.ucsf.edu).
The "measure buriedArea" command does not require picking any blobs. You just specify the parts that you want in the command line. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
So, maybe something like command:
measure buriedarea protein with ligand
...but maybe "ligand" doesn't get your ligand. You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead:
measure buriedarea protein with :UNK
You sent a Pymol session... I don't use Pymol so I can't open that file, sorry. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Chimera
I am sorry to interrupt your busy schedule.
My name is Matsui, and I am a second-year master's student at a Japanese university. Thank you for taking time out of your busy schedule to respond to my question the other day.
We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand.
For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein.
What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time.
In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area.
I tried to check and tried , but it did not work.
1.See https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html
2.Try to use measure blob using chimera X. Reference: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
However, I didn't know how to solve this command. Command ;ui mousemode right "pick blobs
Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html
Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
<Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove LXRβ_1P8D).pse>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Dear Elaine
Thank you for replying.
I'm Matsui.
I apologize for my misunderstanding.
I understand. --------------------------------------------------------------------------- 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9月8日(木) 0:58 Elaine Meng meng@cgl.ucsf.edu:
Dear Kenji, The example commands in my previous message are for ChimeraX, not Chimera. Elaine
On Sep 7, 2022, at 7:06 AM, Kenji MATSUI via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
Dear Elane
Thank you for your time and response.
My name is Matsui, and I am a second-year master's student at a Japanese
university.
I am also using ChimeraX.
But first I will try the method you showed me with chimera, and if it
doesn't work, I will try it with chimeraX as well.
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9月6日(火) 23:30 Elaine Meng meng@cgl.ucsf.edu: Hi Kenji, You are using ChimeraX? I CC'd the ChimeraX address
chimerax-users@cgl.ucsf.edu (different than chimera-users@cgl.ucsf.edu).
The "measure buriedArea" command does not require picking any blobs.
You just specify the parts that you want in the command line.
<
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
So, maybe something like command:
measure buriedarea protein with ligand
...but maybe "ligand" doesn't get your ligand. You would have to use
whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead:
measure buriedarea protein with :UNK
You sent a Pymol session... I don't use Pymol so I can't open that file,
sorry.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera
I am sorry to interrupt your busy schedule.
My name is Matsui, and I am a second-year master's student at a
Japanese university.
Thank you for taking time out of your busy schedule to respond to my
question the other day.
We are investigating the buried surface area to see the magnitude of
the interaction between protein and ligand.
For this purpose, I calculated the solvent accessible area of the
ligand. However, the value is 9955, which shows the entire surface area of the protein.
What should I do? I am not in a hurry for answers , so I would
appreciate a reply when you have the time.
In this case, the ligand was in the binding pocket of the protein, so
I would like to calculate the ligand's solvent contact area = buried surface area.
I tried to check and tried , but it did not work.
1.See
https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html
2.Try to use measure blob using chimera X. Reference:
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea
However, I didn't know how to solve this command. Command ;ui mousemode right "pick blobs
Reference;
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html
Kenji Matsui Graduate School of Tokyo University of Agriculture and Technology M2 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
<Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove
LXRβ_1P8D).pse>_______________________________________________
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription:
https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription:
participants (2)
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Elaine Meng -
Kenji MATSUI