<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Instead of putting a quit/exit command in your script, I
recommend using the --exit option to ChimeraX. That will cause
ChimeraX to exit after the command line arguments are processed.
For example:</p>
<p> chimerax --exit commands.cxc</p>
<p>That has the advantage of not doing any of the web checks for
newer versions of ChimeraX or bundles, so there won't be any extra
popup dialogs or log output. And it let's you use commands.cxc in
an interactive session without it causing ChimeraX to quit.</p>
<p>It's a small tweak that isn't necessary, but you might like it.<br>
</p>
<p> -- Greg<br>
</p>
<div class="moz-cite-prefix">On 9/30/2021 5:20 PM, Tom Goddard via
ChimeraX-users wrote:<br>
</div>
<blockquote type="cite"
cite="mid:AB1953C6-4F3A-474A-A6E4-DE58B06B8998@sonic.net">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Yes I just tested and it runs from the shell with quit command at
end of the file and saves the movie with correct crossfading.
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Sep 30, 2021, at 3:03 AM, Guillaume
Gaullier <<a href="mailto:guillaume.gaullier@icm.uu.se"
class="" moz-do-not-send="true">guillaume.gaullier@icm.uu.se</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<meta http-equiv="Content-Type" content="text/html;
charset=UTF-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; line-break: after-white-space;" class="">
Great, thank you!
<div class="">So, it should also work when running
everything from the shell ($ chimerax
command-file.cxc), right? That would be ideal, since I
like having a quit command at the end of the command
file (not included in my example), allowing me to run
it all from the shell and get my shell prompt back
when the chimerax terminates.
<div class="">
<div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0);
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; text-decoration:
none; word-wrap: break-word; -webkit-nbsp-mode:
space; line-break: after-white-space;" class="">
<div dir="auto" style="caret-color: rgb(0, 0,
0); letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none; word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<div dir="auto" style="caret-color: rgb(0, 0,
0); letter-spacing: normal; text-align:
start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing:
0px; -webkit-text-stroke-width: 0px;
text-decoration: none; word-wrap:
break-word; -webkit-nbsp-mode: space;
line-break: after-white-space;" class="">
<div dir="auto" style="caret-color: rgb(0,
0, 0); letter-spacing: normal; text-align:
start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing:
0px; -webkit-text-stroke-width: 0px;
text-decoration: none; word-wrap:
break-word; -webkit-nbsp-mode: space;
line-break: after-white-space;" class="">
<div dir="auto" style="caret-color: rgb(0,
0, 0); letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space:
normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
text-decoration: none; word-wrap:
break-word; -webkit-nbsp-mode: space;
line-break: after-white-space;" class="">
<div style="letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space:
normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<div style="letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space:
normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;
word-wrap: break-word;
-webkit-nbsp-mode: space;
line-break: after-white-space;"
class="">
<div style="font-family: Helvetica;
font-size: 12px; font-style:
normal; font-variant-caps: normal;
font-weight: normal;
letter-spacing: normal;
text-align: start; text-indent:
0px; text-transform: none;
white-space: normal; word-spacing:
0px; -webkit-text-stroke-width:
0px; word-wrap: break-word;
-webkit-nbsp-mode: space;
line-break: after-white-space;"
class="">
<div style="word-wrap: break-word;
-webkit-nbsp-mode: space;
line-break: after-white-space;"
class="">
<div style="font-family:
Helvetica; font-size: 12px;
font-style: normal;
font-variant-caps: normal;
font-weight: normal;
letter-spacing: normal;
text-align: start;
text-indent: 0px;
text-transform: none;
white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width:
0px;" class="">
<br
class="Apple-interchange-newline">
Guillaume</div>
<div style="font-family:
Helvetica; font-size: 12px;
font-style: normal;
font-variant-caps: normal;
font-weight: normal;
letter-spacing: normal;
text-align: start;
text-indent: 0px;
text-transform: none;
white-space: normal;
word-spacing: 0px;
-webkit-text-stroke-width:
0px;" class="">
<br class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 30 Sep 2021, at 00:31, Tom
Goddard <<a href="mailto:goddard@sonic.net"
class="" moz-do-not-send="true">goddard@sonic.net</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="BodyFragment" style="caret-color:
rgb(0, 0, 0); font-family: Helvetica;
font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; text-align:
start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing:
0px; -webkit-text-stroke-width: 0px;
text-decoration: none;">
<font class="" size="2"><span
style="font-size: 10pt;" class="">
<div class="PlainText">Hi Guillaume,<br
class="">
<br class="">
Ok I fixed crossfade so it will work
during movie recording when the
graphics pane is not shown.<br
class="">
<br class="">
<span
class="Apple-converted-space"> </span><a
href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311" class=""
moz-do-not-send="true">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5311</a><br
class="">
<br class="">
Tom<br class="">
<br class="">
<br class="">
<br class="">
> On Sep 29, 2021, at 11:56 AM, Tom
Goddard via ChimeraX-users <<a
href="mailto:chimerax-users@cgl.ucsf.edu"
class="" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
wrote:<br class="">
><span
class="Apple-converted-space"> </span><br
class="">
> Hi Guillaume,<br class="">
><span
class="Apple-converted-space"> </span><br
class="">
> Thanks for the complete command
script that demonstrates the problem.
From the wrong movie I can see that it
crossfades from entirely black to the
intended image. In testing I find
that it fades from entirely black
(actually in my test it was solid red)
because when the crossfade command is
run it grabs the current image being
shown in the graphics on screen, then
fades that to the next rendered
image. But if you have the file
history thumbnails displayed where the
graphics is normally, then the
apparently graphics was not rendered
to the screen and crossfade gets all
black. If you hide the file history
thumbnails before you open your script
(use the Recent Files toolbar icon, or
the lighting bolt icon in the lower
right corner of main window), then the
movie records correctly.<br class="">
><span
class="Apple-converted-space"> </span><br
class="">
> Usually the file history
thumbnails are hidden automatically
when the first model is opened. I
will have to look at why that is not
happening when opening a script. I
will make a bug report and see if I
can fix that.<br class="">
><span
class="Apple-converted-space"> </span><br
class="">
> Tom<br class="">
><span
class="Apple-converted-space"> </span><br
class="">
><span
class="Apple-converted-space"> </span><br
class="">
>> On Sep 29, 2021, at 2:02 AM,
Guillaume Gaullier via ChimeraX-users
<<a
href="mailto:chimerax-users@cgl.ucsf.edu"
class="" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
wrote:<br class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>> Hello,<br class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>> I am using ChimeraX version
1.2.5 (2021-05-24) on macOS 10.15.7.
When trying to generate a simple movie
with the attached command file, I get
the attached wrong result in which the
crossfade command seems to fail
(instead of a smooth transition, I
only get a flashing black screen for a
few frames). A similar problem happens
with the same version of ChimeraX on
Rocky Linux 8.4.<br class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>> Instead of loading the
command file from a fresh session
(with 'open command-file.cxc'), I
tried to prepare my models first, and
then sent the commands generating the
movie all at once (separated by
semi-colons). When I did it this way,
I got the correct result (also
attached).<br class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>> Is there anything I am doing
wrong, or is this a bug? I am pretty
sure the command file version worked
correctly in a previous version of
ChimeraX, because I have done this
before. Unfortunately, I don’t
remember which version it was (but
probably 1.1, since it was just last
year).<br class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>> I would appreciate any help
with this.<br class="">
>> Thank you in advance,<br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>> Guillaume<br class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>> När du har kontakt med oss på
Uppsala universitet med e-post så
innebär det att vi behandlar dina
personuppgifter. För att läsa mer om
hur vi gör det kan du läsa här:<span
class="Apple-converted-space"> </span><a
href="http://www.uu.se/om-uu/dataskydd-personuppgifter/" class=""
moz-do-not-send="true">http://www.uu.se/om-uu/dataskydd-personuppgifter/</a><br
class="">
>><span
class="Apple-converted-space"> </span><br
class="">
>> E-mailing Uppsala University
means that we will process your
personal data. For more information on
how this is performed, please read
here:<span
class="Apple-converted-space"> </span><a
href="http://www.uu.se/en/about-uu/data-protection-policy" class=""
moz-do-not-send="true">http://www.uu.se/en/about-uu/data-protection-policy</a><br
class="">
</div>
</span></font></div>
<div class="BodyFragment" style="caret-color:
rgb(0, 0, 0); font-family: Helvetica;
font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight:
normal; letter-spacing: normal; text-align:
start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing:
0px; -webkit-text-stroke-width: 0px;
text-decoration: none;">
<font class="" size="2"><span
style="font-size: 10pt;" class="">
<div class="PlainText">>><span
class="Apple-converted-space"> </span><br
class="">
>>
_______________________________________________<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="">
>><span
class="Apple-converted-space"> </span><a
href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"
class="" moz-do-not-send="true">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br
class="">
><span
class="Apple-converted-space"> </span><br
class="">
>
_______________________________________________<br
class="">
> ChimeraX-users mailing list<br
class="">
><span
class="Apple-converted-space"> </span><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="">
><span
class="Apple-converted-space"> </span><a
href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"
class="" moz-do-not-send="true">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br
class="">
<br class="">
</div>
</span></font></div>
<span
id="cid:833211B7E844504F95ED298A5DC0BE4F@user.uu.se"
class=""><command-file.cxc></span><span
id="cid:F6C0ADCF145EB04F89053E92A692E1C6@user.uu.se" class=""><correct-result.mp4></span><span
id="cid:3BF4EB1437835F48900A8D4E21BCAC13@user.uu.se" class=""><wrong-result.mp4></span></div>
</blockquote>
</div>
<br class="">
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
ChimeraX-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX-users@cgl.ucsf.edu</a>
Manage subscription:
<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>
</pre>
</blockquote>
</body>
</html>