On Aug 31, 2022, at 2:34 AM, Kenji MATSUI s214903z@st.go.tuat.ac.jp wrote:

Dear Elaine

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 trying to find out if the ligand (Attached files) can enter the binding pocket.

I would like to calculate the volume of the ligand molecule for this purpose, how should I do this in Chimera ?

What I tried. I tried the one in the two links below and it did not work.

Reference 1.http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005196.html 2.https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#blob

Thank you for your time and support.

---

Kenji Matsui

Hi Kenji,

(1) open ligand structure in Chimera

(2) show molecular surface of ligand, e.g. command: surface

(3) use menu: Tools.. Volume... Measure Volume and Area. This tool automatically shows the area and volume of the surface.

Another way to do the same measurement is with command "measure volume," e.g. if your ligand structure is model #0, command: measure volume #0

The value from the command is shown in Reply Log (menu: Favorites... Reply Log)

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco