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

Thirumurugan Prakasam tp42 at nyu.edu
Mon Feb 24 10:31:02 PST 2020

Thank you soo much for your update and support. I will try.

On Monday, February 24, 2020, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Thiru,
> (I added a subject line to the message so others may be able to find it
> (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
> -----
> 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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Thirumurugan Prakasam,
Research Scientist,
New York University Abu Dhabi,
Experimental Research Building
Building C1, Saadiyat Island
Abu Dhabi, UAE
Phone no: +971-561976358
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