<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. 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. <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. First, make sure you aren't using a very
old version of ChimeraX. I tried it in ChimeraX 1.5
release candidate (2022-11-08) 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. 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. <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> <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. <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="">
-- <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>