<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
</head>
<body>
<p><font face="Calibri">Hi Tom, <br>
</font></p>
<p><font face="Calibri"><font face="Calibri">That is interesting, </font>I
see what you mean. I'll go ahead and update my installation.
Thanks for the explaination!<br>
</font></p>
<font face="Calibri">Best wishes,</font><font face="Calibri"><br>
Caroline</font>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 07/05/2020 17:18, Tom Goddard wrote:<br>
</div>
<blockquote type="cite"
cite="mid:0D3681A5-02BB-4904-BE32-089AA0D9CF3C@sonic.net">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi Caroline,
<div class=""><br class="">
</div>
<div class=""> Tristan is right, although I think the command may
need to be "wait 1" which means draw one frame. (The wait
command without arguments waits until ongoing motions complete
and I'm not sure if it draws a frame when there are no ongoing
motions.) The reason you need to draw a frame is because the
volume surface for your new threshold level is not calculated
until a frame is drawn. In a script graphics are not normally
drawn until the end unless the wait command is used.</div>
<div class=""><br class="">
</div>
<div class=""> We saw this problem before and I put in a fix
where volume surfaces are recomputed when the level changes when
running a script. So your script should work without any
changes in the current ChimeraX daily build. That fix was made
April 7, so I guess you are using a ChimeraX older than that.
I'd suggest updating ChimeraX instead of adding "wait 1" to
your script.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div>
<div class=""><br class="">
</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On May 7, 2020, at 6:02 AM, Tristan Croll <<a
href="mailto:tic20@cam.ac.uk" class=""
moz-do-not-send="true">tic20@cam.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252" class="">
<div style="font-size: 10pt" class="">
<p class="">Try adding the line:</p>
<p class="">wait</p>
<p class="">... before those two commands. That will
tell ChimeraX to draw a frame and do all the
associated processing before moving on.</p>
<div id="signature" class=""> </div>
<p class=""><br class="">
</p>
<p id="reply-intro" class="">On 2020-05-07 13:52,
Caroline Stone wrote:</p>
<blockquote type="cite" style="padding: 0 0.4em;
border-left: #1010ff 2px solid; margin: 0" class="">
<div id="replybody1" class="">
<div class="">
<p class=""><span style="font-family: Calibri;"
class="">Dear All, <br class="">
</span></p>
<p class=""><span style="font-family: Calibri;"
class="">As an exercise in scripting, I am
trying to write a script to imitate the
appearance a published figure (from Toropova
et al 2017). I would like to display a
semi-transparent map which has been color
zoned to match the underlying model in surface
view.<br class="">
</span></p>
<p class=""><span style="font-family: Calibri;"
class="">ChimeraX does everything in the
script apart from the last two commands, in
which I color zone the map, and then make it
transparent. I don't get any errors in the log
to give me a clue what to change. If I omit
these last two commands from the script and
then make them manually from the command line
after the script is finished, it works. Is
there something I can change that would allow
me to include the final two commands in the
script? Any pointers would be much
appreciated. <br class="">
</span></p>
<div class=""><span style="font-family: Calibri;"
class=""> </span><br
class="webkit-block-placeholder">
</div>
<p class=""><span style="font-family: Calibri;"
class=""> # ChimeraX script to imitate
dynein 2 tail Toropova et al 2017 figure style<br
class="">
# Adds custom colours to the ChimeraX
session<br class="">
<br class="">
# Open model and set camera view and model
rotation<br class="">
open 6RLB <br class="">
windowsize 775 775<br class="">
view matrix camera
-0.30533,0.56038,0.76991,623.53,0.82837,-0.24247,0.50499,467.83,0.46967,0.79195,-0.39016,-7.3434
models #1,1,0,0,0,0,1,0,0,0,0,1,0<br class="">
<br class="">
# Work with model representation<br
class="">
surface #1<br class="">
set bgColor white<br class="">
lighting soft<br class="">
graphics silhouettes true<br class="">
<br class="">
# Define custom colours<br class="">
color name midblue #6b80b5<br class="">
color name midgreen #a0c497<br class="">
color name midyellow #f9ef87<br class="">
color name midtomato #f97054<br class="">
color name midmagenta #a4449b<br class="">
<br class="">
# Recolour model using custom colours
defined above<br class="">
select #1/A; color sel midblue<br class="">
select #1/B; color sel skyblue<br class="">
select #1/C; color sel midtomato<br
class="">
select #1/D; color sel midmagenta<br
class="">
select #1/E/F; color sel midgreen<br
class="">
select #1/G/H; color sel lightpink<br
class="">
select #1/I-N; color sel midyellow<br
class="">
select clear<br class="">
<br class="">
# Open map and modify color and
transparency<br class="">
open emdb:4918<br class="">
volume #2 step 1<br class="">
volume #2 level 0.0172<br class="">
surface dust #2 size 10<br class="">
color zone #2 near #1 distance 15<br
class="">
volume #2 transparency 0.75</span></p>
<div class=""><span style="font-family: Calibri;"
class=""> </span><br
class="webkit-block-placeholder">
</div>
<p class=""><span style="font-family: Calibri;"
class="">Best wishes, <br class="">
Caroline<br class="">
</span></p>
</div>
</div>
<br class="">
<div class="pre" style="margin: 0; padding: 0;
font-family: monospace">_______________________________________________<br
class="">
ChimeraX-users mailing list<br class="">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu"
class="" moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br
class="">
Manage subscription:<br class="">
<a
href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"
target="_blank" rel="noopener noreferrer" class=""
moz-do-not-send="true">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
</blockquote>
</div>
_______________________________________________<br
class="">
ChimeraX-users mailing list<br class="">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class=""
moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br
class="">
Manage subscription:<br class="">
<a class="moz-txt-link-freetext" href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br
class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</blockquote>
</body>
</html>