Hi Elaine, Thank you for getting back to me. I have another question. Is it possible to increase the exhaustiveness of Autodock Vina in Chimera? Thank you. With regards, Eunice

On Nov 9, 2021, at 0:53, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Eunice, Not exactly, but if you can "select" a set of residues by any method, e.g. by Ctrl-click-dragging a box around them, or by distance zone from an atom or residue (first select the atom or residue, and then use menu Select... Zone...), then you can write a list of what is selected (menu Actions... Write List...).

Many different ways to select residues: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

Actions menu including Write LIst <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuactions>

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

...

On Nov 8, 2021, at 3:18 AM, Eunice Gwee via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

To whom this may concern, I have been using the Autodock Vina function on Chimera for my studies and I was wondering if it is possible to list the residues in the selected area of the protein used in docking. Thank you. With regards, Eunice

On Jan 28, 2022, at 9:40 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

As the warning ways,

Oops, make that: "As the warning says," Elaine

Hi Eunice, I don't know about boron. Since we are not the developers of Autodock Vina (or Autodock, they are two different programs), better to check on their website and/or publications: <https://vina.scripps.edu/> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 28, 2022, at 8:29 PM, Eunice Gwee via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Elaine,

Thank you for your email. One more thing. I was wondering if boron has been included in the parameterisation of Autodock.

Thank you.

With regards, Eunice