[Chimera-users] Removing structure segment and connecting the edges with dashed line

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 26 15:22:31 PDT 2018

P.S. The distance label could also be removed with command:

setattr p label “ “

(those are just supposed to be two double quotation marks from the keyboard, but it may not work to cut and paste if the Mail app changes them to fancy quotation marks instead)

You can also change color, etc. of the line using either the Selection Inspector (Inspect: Pseudobond or Pseudobond group) or a “setattr p” or “setattr g” command.


> On Jul 26, 2018, at 3:02 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Ahmad,
> The simplest way may be to save the modified structure to a PDB file, then use your favorite text editor remove the “TER” line from the PDB file, and then reopen it in Chimera.
> If you just want to add a dashed line and don’t want to write and reopen a file, another way would be to measure a distance between the atoms on either side of the gap and then hide the distance label.  For example, commands:
> open 1gcn
> delete :10-12
> distance :9 at c:13 at n
> … Ctrl-click the dashed line to select it, then click the green magnifying glass on the bottom right corner of the window to open the Selection Inspector, and then in the Selection Inspector change the label text to nothing (press return to enter the changed value).
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jul 26, 2018, at 11:29 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
>> Hello,
>> Selecting a segment of a structure and deleting it does remove that segment, but the ends are not connected.
>> How to do the same and make the edges connected with a dashed line?
>> Best regards.

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