<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<font face="Times New Roman, Times, serif">Wow, great!<br>
Thanks a lot, Tom!<br>
</font><br>
<div class="moz-cite-prefix">On 18/11/22 21:03, Tom Goddard wrote:<br>
</div>
<blockquote type="cite"
cite="mid:0E433791-D181-4C31-A583-68884B2D3A30@sonic.net">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hi Xavier,
<div class=""><br class="">
</div>
<div class=""> The way to make thicker unit cell lines in
ChimeraX is to show them as cylinders using a "marker model".
If model #3 is the thin line outline then this command will
make the outline with cylinders</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>marker
fromMesh #3 edgeRadius 0.5 color lightyellow</div>
<div class=""><br class="">
</div>
<div class="">Documentation</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a
href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html"
class="moz-txt-link-freetext" moz-do-not-send="true">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/marker.html</a></div>
<div class=""><br class="">
</div>
<div class=""> Tom</div>
<div class=""><br class="">
</div>
<div class=""><img apple-inline="yes"
id="07EAFAD2-C0C7-43EB-969A-359ACDFC9B75"
src="cid:part1.6p0227Yw.iMxU21do@ibmb.csic.es" class=""
width="871" height="496"><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Nov 18, 2022, at 11:31 AM, Elaine Meng via
ChimeraX-users <<a
href="mailto:chimerax-users@cgl.ucsf.edu"
class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; line-break: after-white-space;" class="">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=""><span
id="cid:8192D245-03C6-470A-849C-1CB80C4DAE1A"><Screen
Shot 2022-11-18 at 11.25.32 AM.png></span></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>
</div>
_______________________________________________<br
class="">
ChimeraX-users mailing list<br class="">
<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="">
Manage subscription:<br class="">
<a class="moz-txt-link-freetext" href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br
class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<img src="cid:part2.hiJJI926.CqVTQ314@ibmb.csic.es" border="0"></div>
</body>
</html>