[Chimera-users] Two questions about a model

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 23 09:47:57 PST 2017


Hi Steve,
(1) Labels. Not a silly question, there are just some Chimera quirks!   What you have is a residue label, so  use “Actions… Label… residue… off” (or command “~rlabel”)  rather than "Actions… Label… off” (which is like command “~label”).

You can remove the A, however, by choosing “Actions… Label… residue… custom…” and then using 

%(name)s %(number)s

in the resulting dialog.  You can move the label with the mouse if you first assign some mouse button to do it (menu: Favorites… Preferences, Category: Mouse).  To try this I  changed Ctrl-3 to move-label instead of center-atom.  You can also change label size in the Preferences, Category: Labels.

However, for figures I think the 2D Labels are much better than these “3D labels” that move along with the structure.  The 3D labels are mainly for interactive use, whereas once you have decided upon the view for a specific figure, you can put 2D labels anywhere in the screen, multiple different sizes, colors and fonts (whereas all of the 3D labels have to be the same size and font as each other).  You can just directly enter the text of the 2D label and drag it around with the mouse, without having to use the Preferences.  See Tools… Utilities… 2D Labels  or command “2dlabels”
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html>

Takes a little learning but you can get a much nicer result. Example image attached below.

(2) Those lines are because adjacent residues are displayed and then Chimera tries to show the connectivity with a CA-CA bond.  You can turn this behavior off.  For example, command “select” to select everything, and then click the green magnifying glass icon near the bottom right corner of the Chimera window to open the Selection Inspector.  In that dialog, Inspect: Molecule model and set auto-chaining to “off”.   (Or just use command “setattr m autochain false” but that is probably harder to remember).

For a cleaner appearance, you might also want to hide H atoms, command: ~disp H

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


save
> On Feb 23, 2017, at 2:10 AM, Steven D. Aird <steven.d.aird at gmail.com> wrote:
> 
> Dear Elaine,
> I have a couple of questions about the attached model set.  These are catalytic residues and residues forming the hydrophobic channel in four phospholipases.
> 
> The first question almost seems silly.  I decided to experiment with the label command and labeled one residue in the lower right enzyme of the figure.  I didn’t like the position or form of the label.  I couldn’t get rid of the “.A” on the label and when I tried to delete the entire label, I couldn’t.  Selecting the residue and then selecting LABEL>Off, doesn’t work.
> 
> In all four plots there are fine lines that resemble the earlier ribspline problem, but they are not resolved by "ribspline cardinal.”  Any idea as to what these are?
> 
> As always, thank you for your tutelage.  I am making steady progress.
> Sincerely yours,
> Steve 

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