[Chimera-users] assistance changing pseudobond appearance

Arthur Szabo agszabo at outlook.com
Mon May 1 10:15:02 PDT 2017


My response on Friday was probably premature.

I followed your  instructions and I appeared to have been able to highlight (select) the dashed line that represented the disordered residues. In the Selection Inspector with Pseudobond in the Inspect window, I turned the "halfbond" mode to "off" and double clicked on color, and selected a color "red".
I then used the pulldown menu and selected Inspect Pseudobond group. The color was not what I selected previously so I reselected the color red in that square. I changed the width to 3.0. The width and color within the green selection envelope appears to be correct.

Now the problem: Which button do I select on the bottom of that Selection Inspector window. If I click  on "close" then the dashed line disappears. Strangely if I rotate the image I can sometimes  see it , but  it is very hard  to set the rotational position where the dashed line is visible.

Alternately if I go to select on the main menu, and click on clear selection the dashed  line totally disappears.

So I appear to be stuck. Not sure if clicking on "close" on the Selection Inspector was the right thing to do.



-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Friday, April 28, 2017 3:52 PM
To: Arthur Szabo <agszabo at outlook.com>
Cc: chimera-users at cgl.ucsf.edu BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] assistance changing pseudobond appearance

Hi Arthur,
First Ctrl-click on the dashed line to select it.  Then, click the green magnifying glass icon near the bottom right of the Chimera window to open the Selection Inspector.  In the Inspector window (Inspect: Pseudobond):
(1) change  “halfbond mode” to “off”, otherwise it will get colored by the atoms instead of having its own color
(2) click or doubleclick the square color thing to make the Color Editor window appear, in which you can change the color

To make the dashed line fatter, stay in the Inspector tool but now use pulldown menu to Inspect: Pseudobond group (instead of just Inspect: Pseudobond), then:
change “line width” to some bigger number

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

> On Apr 28, 2017, at 12:16 PM, Arthur Szabo <agszabo at outlook.com> wrote:
> I asked this question several months ago, but rarely have applied the answer. 
> I have a structure that has a long stretch that is disordered. In the  structure it appears as a dashed line. 
> If I highlight this section of the total sequence and then apply a color (red) the whole structure is then colored red.
> So how can I make  the dashes slightly larger, and secondly color that stretch of dashes with a particular color without coloring the rest of the molecule? 
> Thank you
> Arthur G. Szabo

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