[Chimera-users] Save as GIF (animated or otherwise)

Oliver Clarke olibclarke at gmail.com
Tue Apr 26 10:25:28 PDT 2016

Thanks Cristina! That's pretty much exactly what I'm looking for (I guess
the ppms or pngs can be converted to mp4 subsequently).

It doesn't seem to work though when entered under the "additional encoding
options" section of the "Record Morph Map" dialog (as "movie encode
resetMode keep"), I guess either it only works in a script or I am using
the incorrect command.

Re the transparent background you mean for movie frames or regular still
images? For the latter the "Transparent background" checkbox in the "Save
image" dialog works fine, for the former I am not sure.


On Tue, Apr 26, 2016 at 1:10 PM, Cristina Paulino <c.paulino at bioc.uzh.ch>

> Hi Oliver,
> To save the frames there is the option "resetMode". Its default is clear
> which will delete all the frames once the movie has converted. However if
> you use the command "resetMode keep" or "resetMode none" the frames will be
> saved. There is also the option to indicate in which file format the frames
> will be saved and you can even indicate a sub folder as path to save them.
> You find most of the options I mentioned here:
> https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/movie.html
> Best
> Cristina
> PS for editing purposes later I would like to have a transparent
> background. However all the option that I have found so far did not work.
> Has anyone successfully experienced doing it?
> On 26.04.2016, at 19:01, Oliver Clarke <olibclarke at gmail.com> wrote:
> Looking into it further "animated PNGs" are apparently a thing that
> exists, but they can't be edited with GIMP and the range of tools that one
> can use to interconvert GIFs with e.g. MP4s does not seem to exist.
> Cheers,
> Oli
> On Tue, Apr 26, 2016 at 12:50 PM, Oliver Clarke <olibclarke at gmail.com>
> wrote:
>> For ease of editing. I don't know an easy way to edit MP4 files frame by
>> frame and add labels etc, whereas it is straightforward for GIF files, and
>> for many animations (e.g. a simple density map or model morph) I don't need
>> more than 256 colors. If animated jpegs or png exist I would be happy with
>> that too, but I wasn't aware of such.
>> Cheers,
>> Oli
>> On Tue, Apr 26, 2016 at 12:20 PM, Greg Couch <gregc at cgl.ucsf.edu> wrote:
>>> Why GIF?  Typical GIFs are limited to 256 colors.  Why not PNG, which is
>>> full color, compressed and lossless?  Or JPEG which is full color and
>>> compressed even more?  Ideally, there should be no new GIF format files.
>>>     -- Greg
>>> On 4/26/2016 8:55 AM, Oliver Clarke wrote:
>>> Hi,
>>> It would be very useful if Chimera (prob ChimeraX) was able to save
>>> either single frames, or, preferably, record movies in GIF format.
>>> This is not so much out of a desire to make animated gifs (although
>>> these can be handy for presentations and use on the web), but more because
>>> it makes it very easy to create labeled movies in vector graphics programs
>>> (one can edit a single frame in a vector graphics program and then insert
>>> it and alter the duration in for example GIMP or similar), which can then
>>> be easily converted back to mp4. Otherwise adding labels and custom
>>> annotations to movies is a pain for a novice like me, though if any one has
>>> any suggestions for recommended software I'd love to hear them! I've tried
>>> using iMovie and found it incredibly frustrating for the kinds of simple
>>> things like to do - adding labels, boxes, arrows etc to highlight specific
>>> domains during a morph, for example.
>>> At the moment I make a movie in chimera and convert it to a GIF using
>>> videoblend, edit in affinity designer and GIMP and then convert back to mp4
>>> using online tools, but a more direct route would definitely be useful.
>>> Cheers,
>>> Oliver.
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