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<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="">Â 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="">Â 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. 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=""><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: Â 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
  <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="">
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</blockquote>
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</blockquote>
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</blockquote>
<br>
<div class="moz-signature">-- <br>
<img src="cid:part2.hiJJI926.CqVTQ314@ibmb.csic.es" border="0"></div>
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