[Chimera-users] display vectors

[Eric Pettersen]

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 <mailto: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 <mailto:m.kadlof at cent.uw.edu.pl>>
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