[Chimera-users] adding dashed lines, showing transparent spheres

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 24 09:17:46 PST 2020

Hi Thiru,
(I added a subject line to the message so others may be able to find it later.)

(A) There are a couple ways to add a dashed or dotted line, but one easy way if you only need to add a few is to first just make distance measurements, and then hide the distance values.  For example, show Distances tool (menu: Tools… Structure Analysis… Distances).  Then for each line you want to add, Ctrl-click one atom to select it, Shift-Ctrl second atom to select it …. now there are two atoms selected and you can add the line between them by clicking the “Create” button on the Distances tool.

With the Distances tool you can set “Labels” to “None” and change the distance color, line width, and line style.

You should do this when only one copy of the structure is open, and shown as sticks.  Part (B) below   describes opening a second copy to show the spheres, and if you do that first, you will have to use Model Panel to hide the spheres model temporarily (uncheck the “S” box) so that you can add the distance measurements to the sticks.

(B) To show transparent spheres and sticks at the same time, open the same structure twice.  Then show one copy as spheres and make it partially transparent.  For example, commands:

open pubchem:448537
open pubchem:448537
repr sphere #1
trans 50 #1
set bg_color white


The 50 means 50% transparent.  You could use some other value.  Also you could change the colors of the spheres (model #1 in this example) and sticks (model #0 in this example) as you like.

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

> On Feb 23, 2020, at 4:11 AM, Thirumurugan Prakasam <tp42 at nyu.edu> wrote:
> Hi,
> I am trying to make metal coordination bond as a dotted line and also I need to make electron clouds around the atoms as in the picture below (Please provide me short guidelines on how to make nice cartoon). Please help me sort this two issues.
> Looking forward to hearing from you,
> Many thanks,
> Thiru
> <image.png>
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