<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<font face="Times New Roman, Times, serif">Ok, thanks anyhow,
Elaine!<br>
I think I could get a workaround: select the box and treat it as a
surface, then activate silhouette.<br>
Best,<br>
Xavier<br>
</font><br>
<div class="moz-cite-prefix">On 18/11/22 20:31, Elaine Meng wrote:<br>
</div>
<blockquote type="cite"
cite="mid:2115C000-E260-4CDB-95F1-66B0BBC2FAEA@cgl.ucsf.edu">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
Hrmmm... maybe this does not solve the problem. In my experiment,
it didn't work well on the unit cell box. Â It does work for other
selections like on ribbons, but there is a gap between the unit
cell box line and the selection highight lines, at least on my
computer:
<div class=""><br class="">
</div>
<div class=""><img apple-inline="yes"
id="32DEC02E-D9F3-41ED-9DB8-4EB2F743CCDA"
src="cid:part1.YgJdEqBi.7YYkifBL@ibmb.csic.es" class=""
width="390" height="341"></div>
<div class=""><br class="">
</div>
<div class="">I showed the unit cell box outline as magenta and
then used command:  graphics selection color magenta width 5</div>
<div class=""><br class="">
</div>
<div class="">So maybe there isn't any good way of doing it other
than maybe postprocessing in some image-editing program like
gimp or Photoshop.</div>
<div class="">Sorry about that,</div>
<div class="">Elaine<br class="">
<div class=""><br class="">
</div>
<div class=""><br class="">
<blockquote type="cite" class="">On Nov 18, 2022, at 11:04 AM,
Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu"
class="moz-txt-link-freetext" moz-do-not-send="true">meng@cgl.ucsf.edu</a>>
wrote:<br class="">
<br class="">
(switching to chimerax-users address since this is all about
ChimeraX, not Chimera)<br class="">
<br class="">
Sorry no, there is no linewidth setting on the unit cell
outline box.<br class="">
<br class="">
However, you can "fake it" by selecting that model so that
there are green outlines to show the selection, and then
changing the selection-outline color and width:<br class="">
<br class="">
(1) select the outline box model, e.g. as described in the
previous message by checking the selection box in the Model
Panel<br class="">
<br class="">
(2) use "graphics selection" command to change the
selection-outline color and thickness<br class="">
<<a
href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection"
class="moz-txt-link-freetext" moz-do-not-send="true">https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection</a>><br
class="">
<br class="">
I hope this helps,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D. Â Â Â Â Â Â Â Â Â Â Â Â <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On Nov 18, 2022, at 9:12
AM, F.Xavier Gomis-Rüth via Chimera-users <<a
href="mailto:chimera-users@cgl.ucsf.edu"
class="moz-txt-link-freetext" moz-do-not-send="true">chimera-users@cgl.ucsf.edu</a>>
wrote:<br class="">
<br class="">
Thanks a lot, Elaine, this worked indeed!<br class="">
Just one final point: how can I make the linewidth larger?
When I make a picture, the thin lines of the box
disappear.<br class="">
I understand ChimeraX interpretes these lines as a
surface, I can change the colour when choosing surface in
the colour blow up.<br class="">
<br class="">
On 18/11/22 17:49, Elaine Meng wrote:<br class="">
<blockquote type="cite" class="">Hi Xavier,<br class="">
As far as I can tell, it is exactly the same in ChimeraX
as in Chimera. Â First, make sure you aren't using a very
old version of ChimeraX. Â IÂ tried it in ChimeraX 1.5
release candidate (2022-11-08) Â just now:<br class="">
<br class="">
- open your structure that has unit cell information,
e.g. 1fav<br class="">
<br class="">
- in Unit Cell tool (menu: Tools... Higher-Order
Structure... Unit Cell) click Outline to show unit cell
box<br class="">
<br class="">
- if you want to change box outline color, can use the
same method as described below for Chimera. I wasn't
able to select it by Ctrl-click, however, so instead use
the selection (hand with green dot) checkbox in the
Model Panel to select it, then use Actions... Color...
[...].   Or, you can just click the color square in the
Model Panel and use the system color chooser to change
the color interactively. Â Screenshot:<br class="">
<br class="">
<Screen Shot 2022-11-18 at 8.48.02 AM.png><br
class="">
<br class="">
<br class="">
I hope this helps,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D. Â Â Â Â Â Â Â Â Â Â Â Â <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
P.S. for ChimeraX questions specifically, you may want
to use the other mailing list, <a
href="mailto:chimerax-users@cgl.ucsf.edu"
class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>Â <br
class="">
<br class="">
<blockquote type="cite" class="">On Nov 18, 2022, at
7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <<a
href="mailto:chimera-users@cgl.ucsf.edu"
class="moz-txt-link-freetext" moz-do-not-send="true">chimera-users@cgl.ucsf.edu</a>>
wrote:<br class="">
<br class="">
Dear Elaine,<br class="">
I am now trying to get this done in ChimeraX where
there is indeed a similar option. Unfortunately, if I
proceed as in the instructions<br class="">
I do not get the cell box, in contrast with old
Chimera. I also tried through the command line but
unsuccessfully.<br class="">
Am I missing something?<br class="">
Thanks a lot in advance,<br class="">
Xavier<br class="">
<br class="">
On 26/10/22 17:45, Elaine Meng wrote:<br class="">
<blockquote type="cite" class="">Hi Xavier,<br
class="">
You can select the box (Ctrl-click on it) and then
use menu: Actions... Color... [choose color], then
clear selection by Ctrl-click on blank area of
window or menu Select... Clear Selection.<br
class="">
I hope this helps,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D. Â Â Â Â Â Â Â Â Â Â Â Â <br
class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On Oct 26, 2022, at
1:56 AM, F.Xavier Gomis-Rüth via Chimera-users
<<a href="mailto:chimera-users@cgl.ucsf.edu"
class="moz-txt-link-freetext"
moz-do-not-send="true">chimera-users@cgl.ucsf.edu</a>><br
class="">
wrote:<br class="">
<br class="">
Dear all,<br class="">
is there a way in Chimera or ChimeraX to get the
unit-cell box being drawn in another colour than
white?<br class="">
This forces the background to be dark....<br
class="">
Thanks a lot in advance,<br class="">
Xavier<br class="">
<br class="">
</blockquote>
</blockquote>
<br class="">
</blockquote>
<br class="">
</blockquote>
<br class="">
--Â <br class="">
<fxgr_signanew.jpg><br class="">
_______________________________________________<br
class="">
Chimera-users mailing list: <a
href="mailto:Chimera-users@cgl.ucsf.edu"
class="moz-txt-link-freetext" moz-do-not-send="true">Chimera-users@cgl.ucsf.edu</a><br
class="">
Manage subscription: <a
href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users"
class="moz-txt-link-freetext" moz-do-not-send="true">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a><br
class="">
</blockquote>
<br class="">
</blockquote>
<br class="">
</div>
</div>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<img src="cid:part2.TpxfG0vi.uJbWuq0q@ibmb.csic.es" border="0"></div>
</body>
</html>