Removing structure segment and connecting the edges with dashed line
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.
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@c:13@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@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. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> Elaine
On Jul 26, 2018, at 3:02 PM, Elaine Meng <meng@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@c:13@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@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.
participants (2)
-
Ahmad Khalifa -
Elaine Meng