Dear Kenji, You have many more than 2 atoms selected. You can see from the green outlines that you have the whole residue of Trp selected (multiple atoms) and 1 atom of the ligand. You need to pick only 1 atom from ligand and 1 atom from Trp. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 27, 2022, at 6:59 PM, Kenji MATSUI via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear Chimera X

Thank you very much for your kind answers.

I tried to find the distance between ligand(cluster14) and protein(TRP420) by referring to the tutorial, but I could not do it, so I contacted you.

Detail Objective: To display the distance between cluster14 and TRP420(The area circled in yellow）. <image.png> I chose cluster 14 and TRP420 (shift+ctrl+click)→tool →structure Analysis →distance

Refernece:　Chimera tutorial To measure distances: ・Select two atoms – press Shift + Control + Left click on the atoms in the graphics window >> ・ Tools >> Structure Analysis >> Distances >> Create - Distance reported in graphics and new window

But, error is shown. How to solve this problem? <image.png>

<image.png>

What else I tried.

combine ligand and protein(OSBP)→But, I couldn't display.