Using Per-Frame commands to recolor structures with attribute data is very slow
Hi, As a follow up to this thread (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003712.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003712.html>) from 2009, I’d like to color a model by a custom attribute that changes from frame to frame. Using the workaround mentioned in that thread, we are able to use Per-Frame commands to load a new attribute file each frame, and then color the structure by the attribute, but this awfully slow (probably over 1 second per frame). Is there a way to cache the attribute data? Or a way to improve the performance of defining the attributes and re-coloring the structure? I know that I could use a Python script to load each coordinate frame with its associated attribute data, save images, and then stitch them together for a movie, but the current goal is for data exploration.
Hi David, An approach to make the playback faster is to define all your frame-attr data at once by make one big defattr file that is basically all your attribute files concatenated together, but with the attribute names changed to append the corresponding frame number, i.e. a file that defines myattr1, myattr2, etc. Then in your perframe command, use $1 to add the frame number to the end of the attr name. So while the defattr part of your process will be considerably slower, the playback will be faster. This approach has the additional advantage that if you save a session, all the attribute definitions will be preserved and you won’t need to redefine them. —Eric Eric Pettersen UCSF Computer Graphics Lab On Nov 26, 2018, at 8:49 PM, David Slochower <slochower@gmail.com> wrote:
Hi,
As a follow up to this thread (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003712.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003712.html>) from 2009, I’d like to color a model by a custom attribute that changes from frame to frame. Using the workaround mentioned in that thread, we are able to use Per-Frame commands to load a new attribute file each frame, and then color the structure by the attribute, but this awfully slow (probably over 1 second per frame).
Is there a way to cache the attribute data? Or a way to improve the performance of defining the attributes and re-coloring the structure? I know that I could use a Python script to load each coordinate frame with its associated attribute data, save images, and then stitch them together for a movie, but the current goal is for data exploration. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Eric. I was able to define all the attributes at once, as you suggested, and this does make things a lot faster, although recoloring still slows down playback. Thanks for the tip!
On Nov 27, 2018, at 10:43 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi David, An approach to make the playback faster is to define all your frame-attr data at once by make one big defattr file that is basically all your attribute files concatenated together, but with the attribute names changed to append the corresponding frame number, i.e. a file that defines myattr1, myattr2, etc. Then in your perframe command, use $1 to add the frame number to the end of the attr name. So while the defattr part of your process will be considerably slower, the playback will be faster. This approach has the additional advantage that if you save a session, all the attribute definitions will be preserved and you won’t need to redefine them.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 26, 2018, at 8:49 PM, David Slochower <slochower@gmail.com <mailto:slochower@gmail.com>> wrote:
Hi,
As a follow up to this thread (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003712.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003712.html>) from 2009, I’d like to color a model by a custom attribute that changes from frame to frame. Using the workaround mentioned in that thread, we are able to use Per-Frame commands to load a new attribute file each frame, and then color the structure by the attribute, but this awfully slow (probably over 1 second per frame).
Is there a way to cache the attribute data? Or a way to improve the performance of defining the attributes and re-coloring the structure? I know that I could use a Python script to load each coordinate frame with its associated attribute data, save images, and then stitch them together for a movie, but the current goal is for data exploration. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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Eric Pettersen