The charge computation that Chimera carries out is actually performed by a separate program (antechamber, from AmberTools). On Windows, as antechamber executes, that black window appears and will disappear when antechamber finishes. The computation takes awhile on a molecule as big as the one you're using. On my 2015 Mac it take 87 seconds to finish. At any rate, the black window is nothing to worry about.

On Jan 9, 2023, at 6:38 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 interactions between protein and ligand.

I want to optimize the attached file compound. I want to adjust the charge for this purpose.

<image.png>

Question
However, when I press OK in the first photo section, a black screen appears as in the second photo.In you tube and other videos, I was moved to the save etc. screen. Is the charge optimization done correctly here?

<image.png>

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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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