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<font size="4"><font face="monospace">Hi, <br>
<br>
we use the mseries a lot to compare maps and create movies. <br>
It is really great and allows for preliminary observations. Now
that we are now moving in more detailed examinations, I can see
where Oliver's query goes and is interesting. I also think it's
not a niche but the future of cryoEM observations. <br>
<br>
More tools along these lines could only be an asset. <br>
Best<br>
Vincent<br>
</font></font><br>
<div class="moz-cite-prefix">Le 02/02/2022 à 21:58, Tom Goddard via
ChimeraX-users a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:DE346E73-FA40-4803-BCF6-6005F2A84267@sonic.net">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<div>Hi Guillaume,</div>
<div><br class="">
</div>
<div>The row of checkbuttons (default 10 buttons one for each
model) will not handle 50 maps unless you have an extremely wide
screen (about two normal screens wide) with Chimera shown full
width. I don't understand how it is useful for comparing many
maps since I have not used it. Of course often we have dozens
of data sets open and compare them. For example the tile
command can show them all in a rectangular grid, and there are
many many other ways.</div>
<div><br class="">
</div>
<div>Have you used the Chimera "displayed models" and "skip
models" check buttons below the command-line?</div>
<div><br class="">
</div>
<div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 2, 2022, at 12:42 PM, Guillaume Gaullier
<<a href="mailto:guillaume.gaullier@icm.uu.se"
class="moz-txt-link-freetext" moz-do-not-send="true">guillaume.gaullier@icm.uu.se</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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charset=UTF-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
line-break: after-white-space;" class="">
Hi,
<div class=""><br class="">
</div>
<div class="">Just to confirm that this is also my
experience with cryoEM. For very straightforward
projects, you can get away with only a handful of maps
(I typically request 4 from normal 3D classification).
But once you’re using advanced methods to analyze
heterogeneity (like cryoSPARC 3DVA or cryoDRGN), it is
very common to have to examine 50 maps or more every
time you get results from a new job, and you rarely run
a single job. Having more ways to navigate multiple maps
can only help!</div>
<div class=""><br class="">
</div>
<div class="">Cheers,<br class="">
<div class="">
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<br
class="Apple-interchange-newline">
Guillaume</div>
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<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 2 Feb 2022, at 20:37, Oliver Clarke
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="">
<div class="">Hi Tom,</div>
<div class=""><br class="">
</div>
It is increasingly not niche at least for single
particle cryo-EM folks - pretty much all of us
deal with the issue of comparing many classes,
or sets of classes, in the context of one or
more atomic models. Anything that facilitates
that is useful to most of us in the field these
days in my experience. Believe me if I had the
faintest idea how to add it in I would do so! :)
<div class=""><br class="">
</div>
<div class="">Cheers</div>
<div class="">Oli<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 2, 2022, at 2:34 PM,
Tom Goddard <<a
href="mailto:goddard@sonic.net"
class="moz-txt-link-freetext"
moz-do-not-send="true">goddard@sonic.net</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="">
Got it. Never knew about that "skip
in previous/next" row in the Chimera
daily build. Seems really like a
niche feature but I understand it is
useful to you. This is the kind of
feature that is so special purpose
that it would be good candidate for
someone who really benefits from it to
implement it as a ChimeraX plugin.
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Tom</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Feb 2, 2022, at
11:20 AM, Oliver Clarke 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="">
Hi Tom, right - in
recent-ish nightly builds of
Chimera Eric added another
row - "skip in
previous/next" which allows
one to control which models
are excluded from the
sequence.
<div class=""><br class="">
</div>
<div class="">So in the
attached picture, models
3&4 would be excluded
from the sequence - #3
would always be displayed,
while #4 would always be
hidden. This is very
useful to be able to do on
the fly, when one is
comparing lots of
different models & 3D
classes that are aligned
to one another.
<div class=""><br class="">
</div>
<div class="">Cheers</div>
<div class="">Oli</div>
<div class="">
<div class=""><br
class="">
</div>
<div class=""><span
id="cid:7F759D57-DE4D-480E-B57B-A0128F079CCF"
class=""><PastedGraphic-1.png></span><br
class="">
<div class=""><br
class="">
<blockquote
type="cite"
class="">
<div class="">On
Feb 2, 2022, at
2:11 PM, Tom
Goddard <<a
href="mailto:goddard@sonic.net"
class="moz-txt-link-freetext" moz-do-not-send="true">goddard@sonic.net</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="">
Hi Oliver,
<div class=""><br
class="">
</div>
<div class="">
You are right
the ChimeraX
mseries
command does
not allow you
to easily
remove or add
models to the
sequence if
models that
the slider
displays.
Could you
explain how
that works in
Chimera? I
guess you are
referring to
the optional
row of
"Displayed
model"
checkbuttons
below the
command line
in Chimera
that can be
shown using
command-line
preferences
and has Next
and Previous
buttons. But
I don't
understand how
that lets you
change which
models you
cycle through
-- doesn't it
always cycle
through all
models in
model number
order? Eric
implemented
that Chimera
feature and
maybe I just
don't
understand how
it works.</div>
<div class=""><br
class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Tom<br
class="">
<div class=""><br
class="">
<blockquote
type="cite"
class="">
<div class="">On
Feb 2, 2022,
at 8:43 AM,
Oliver Clarke
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="">
I've played
with this a
bit now Tom
and I still
think the
Chimera
implementation
is superior
for some use
cases, as it
is more
flexible - it
is easy to
remove or add
volumes or
models to the
series "on the
fly", whereas
in ChimeraX
this needs to
be done when
creating the
series (unless
I am missing
something
which is
entirely
possible!).
<div class=""><br
class="">
</div>
<div class="">It
would be great
to have at
some point an
implementation
of a "default"
model/volume
series as
exists in
Chimera, where
one can click
next/prev or
have an option
to temporarily
add/remove
each model
from the
series.
<div class=""><br
class="">
</div>
<div class="">Cheers</div>
<div class="">Oli<br
class="">
<div class=""><br
class="">
<blockquote
type="cite"
class="">
<div class="">On
Sep 29, 2021,
at 3:30 PM,
Tom Goddard
<<a
href="mailto:goddard@sonic.net"
class="moz-txt-link-freetext" moz-do-not-send="true">goddard@sonic.net</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="">
Hi Oli,
<div class=""><br
class="">
</div>
<div class="">
The "mseries
slider"
command in
ChimeraX
provides a
related
capability to
flip through
several models
using a
slider, for
example,</div>
<div class=""><br
class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>mseries
slider
#1-5,7-12</div>
<div class=""><br
class="">
</div>
<div class="">allows
displaying one
of the
specified
models without
effecting the
display of
models that
are not listed
in the
command.</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/mseries.html"
class="moz-txt-link-freetext" moz-do-not-send="true">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html</a></div>
<div class=""><br
class="">
</div>
<div class="">
Tom</div>
<div class=""><br
class="">
</div>
<div class=""><br
class="">
<div class=""><br
class="">
<blockquote
type="cite"
class="">
<div class="">On
Sep 29, 2021,
at 9:42 AM,
Oliver Clarke
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="">
Hi,
<div class=""><br
class="">
</div>
<div class="">The
Next/Previous
buttons in
original
Chimera,
combined with
the capacity
to lock the
display status
of one model
(using the
"Skip")
checkboxes,
are really
useful when
comparing
multiple maps
(particularly
multiple
aligned maps
with a single
atomic model),
and I really
miss this
functionality
in ChimeraX...
would it be
possible to
add it to the
(diminishing!)
list of
features to
port over?</div>
<div class=""><br
class="">
</div>
<div class="">Cheers</div>
<div class="">Oli</div>
<div class="">
<div class=""><br
class="">
</div>
<div class="">PS
My mind was
blown
yesterday when
I found out
that ChimeraX
has
(universal?)
undo/redo
bound to
hotkeys! Would
it be possible
to add the
option of user
defined
hotkeys...?
E.g. for
invoking a
custom
function,
style,
lighting etc?</div>
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