[Chimera-users] display vectors

[Michał Kadlof]

Works like a charm! :D

Thank you!

--
pozdrawiam serdecznie
Michał Kadlof <m.kadlof at cent.uw.edu.pl>

2018-05-23 19:56 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:

> Okay, I can reproduce it now. It’s because the script itself is extremely
> long.  Chimera is:
>
> 1) Breaking the script into lines
> 2) Looking for lines that start with ‘#*frame_number*:’ and removing that
> part
> 3) Joining the lines back together
> 4) Substituting instances of ‘<FRAME>’ with the current frame number
> 5) Handing the result off to the command-script processing code for actual
> execution
>
> For a big script, that is slow.  I suggest you put your commands into
> separate files with the frame number embedded in their names (eg. cmd.457),
> and change your script to simply be “read ~/cmd_folder/cmd.<FRAME>”.
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
> On May 23, 2018, at 10:28 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> Hi Michał,
> We cannot reproduce the slow playback you’re getting with the per-frame
> cones.  Our guess is that it’s something else with the trajectory that’s
> problematic.  Does it have a large nucleic acid in it (with abstracted
> “Nucleotides” depiction?).  Do you have a molecular surface present (even
> if hidden [check the Model Panel])?
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
> On May 23, 2018, at 7:41 AM, Michał Kadlof <m.kadlof at cent.uw.edu.pl>
> wrote:
>
> Hi,
>
> I'm running MD simulation and I would like to display forces vectors
> "live". My strategy is to run:
>
> MD Movie -> PerFrame Script -> In this script create a shape (cone), and
> update it every frame. I transformed my vectors into ration axis and angle,
> and run it. However it works extreamly slow, and even lowering quality of
> cone didn't help. Do you have any clues?
>
> Here is how my script looks like:
>
> #1: close #1; shape cone radius 0.2 height 3.051701874476991 center :47
> divisions 10 color red rotation 1.003198923120698,-0.8433298543660601,-0.
> 5373867542336597,180
> #2: close #1; shape cone radius 0.2 height 3.054021942152826 center :47
> divisions 10 color red rotation 1.0022878678774028,-0.8433406134841704,-0.
> 5373745205242975,180
> #3 ...
>
> --
> pozdrawiam serdecznie
> Michał Kadlof <m.kadlof at cent.uw.edu.pl>
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