Elaine Thank you for your prompt reply. I should probably ask another question going through the generic question email. But In the structure I am working with there is a 25 amino acid segment that is flexible and not represented in the crystal structure. In the Chimera structure it is represented by a series of dashed lines. How can I increase the thickness of those branched lines and even change their color from the rest of the protein. Thank you Arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: January-14-16 7:13 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: coloring only specific atoms, or atoms but not ribbon Hi Arthur, If you are coloring your selection with the menu, choose menu: Actions… Color… all options (it’s at the bottom of the menu). That will open a separate Color Actions dialog, in which you could set the “Color applies to” to “atoms/bonds” to color atoms/bonds only, or “ribbons” to color ribbon segment only, etc. (default is “all of the above”). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/coloractions.html> If you first display the atoms of the residue, you can Ctrl-click to select a specific atom instead of the whole residue. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect> If you are using the “color" command, you control which types of displays are affected by putting some text right after the color name. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/color.html> For example: color red,a sel …. which colors atoms/bonds only, indicated by the “,a” (no space before it!!), and instead of selecting and using “sel” you can give residue and atom information directly: color red,a :55.A@ND1 … to color atom ND1 of residue 55 in chain A, or color hot pink,r :55.A … to color ribbon-only (indicated by “,r”) of residue 55 in chain A The getting-started tutorials include examples of these, but I know it can be hard to find exactly what you want. <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 14, 2016, at 1:59 PM, A G Szabo <agszabo@bell.net> wrote:

I have to admit that my understanding of the various commands to use for very specific functions in Chimera is difficult for me to find the correct command.

I know how to color a specific residue using the sequence table and the color chart. So how do I color a specific atom in a residue. For example I am interested in coloring the nitrogen of the Asn amide side chain say color red. How can I do this? When I highlight a residue and visualize it as a ball and stick, then color it different from the color of the helix, the color of that part of the helix changes to the color of the ball and stick, different from the color of the rest of the helix.

How can I reset the color of the helix location of that residue, leaving the ball and stick as another color. Thank you

Arthur Szabo Professor Emeritus Chemistry and Biochemistry Wilfrid Laurier University Waterloo Canada.

Elaine Thank you for your prompt reply. I should probably ask another question going through the generic question email. But

In the structure I am working with there is a 25 amino acid segment that is flexible and not represented in the crystal structure. In the Chimera structure it is represented by a series of dashed lines. How can I increase

Elaine Once again you have been very helpful. Thank you very much. It worked. I`ll Have to remember to send you a copy of the book when it is completed. arthur -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: January-15-16 2:07 PM To: A G Szabo Cc: chimera-users@cgl.ucsf.edu Subject: changing appearance of dashed lines Hi Arthur, Those dashed lines are "pseudobonds" (like H-bond and distance-measuring lines). You can Ctrl-click to select one and then click the green magnifying glass icon near the bottom right of the Chimera window to show the Selection Inspector. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html> In the Selection Inspector, you can Inspect "Pseudobond" and change its color by: (1) turning "halfbond mode" to "off", AND (2) clicking on the square color-well and using the resulting Color Editor dialog to choose a color. The color will not be visible in the display unless you turn halfbond mode off. To change line thickness, Inspect "Pseudobond group" (click on the "Pseudobond" and you can see it is a menu where you can change to "Pseudobond group" instead) and then change the "line width" value. Or, you could do all these things with the "setattr" command <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> .of which there are a few examples in these previous posts: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010614.html> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010615.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 14, 2016, at 6:27 PM, A G Szabo <agszabo@bell.net> wrote: the thickness of those branched lines and even change their color from the rest of the protein.

Thank you Arthur