[Chimera-users] Thermal ellipsoids are not updated when playing multi-frame PDB trajectory

Eric Pettersen pett at cgl.ucsf.edu
Thu Mar 31 12:48:36 PDT 2011

On Mar 31, 2011, at 6:59 AM, Lukasz Walewski wrote:

> Hi,
> I am looking at the trajectory with thermal anisotropy factors that
> change from frame to frame, i.e. I have a multi-frame PDB file that
> contains ATOM and ANISOU records. The components of the anisotropy
> tensors change during the simulation (the data I am analyzing has a
> redefined meaning). I am able to properly read and play the  
> trajectory.
> Ellipsoid representation of the thermal U factors works excellent  
> for a
> single frame. However it seems that the ellipsoids are not updated  
> when
> I play the trajectory, i.e. the atoms move as expected but the
> ellipsoids retain both their positions and shape from the first frame.
> Is there any way around ?

Hi Lukasz,
	Chimera doesn't store any info on a per-frame basis right now, so the  
shortest answer is no.  However, depending on the size of the system  
you are working with and the length of your trajectory (and your  
patience!) there may be a workaround.  Basically the workaround is to  
read your trajectory file using the regular FIle..Open dialog rather  
than with the trajectory tool.  This will cause each MODEL in your  
file to be opened as a separate model in Chimera.  This consumes a lot  
more memory than the trajectory would, so I would say it is practical  
if we are talking dozens of models or less, or hundreds of models if  
your system is no more than 1000 atoms or so, or a few thousand models  
if we're talking about a small molecule.
	Of course you lose the convenience of the MD Movie's playback  
interface.  Nonetheless, you can get a poor man's playback with a  
script like this:

aniso parameters-you-want
modeldisp #0.1; some-timing-command
~modeldisp #0.1; modeldisp #0.2; some-timing-command
~modeldisp #0.2; modeldisp #0.3; some-timing-command

Hopefully you or someone you know is familiar with programming, which  
would allow you to create such a script easily rather than by insanely  
tedious hand editing.  You run the script either with File...Open or  
the "open" command.  The script file name should end in ".cmd" or  
	A couple of points about the script:
1) Commands on the same line separated by semi-colons are executed  
without the screen being redrawn between commands.
2) There are a couple of choices for "some-timing-command":
	a) "wait N" where N is an integer.  In that case Chimera will wait  
that many thirtieths of a second before going on to the next command.   
So "wait 15" would pause half a second before going on to the next  
command.  Keep in mind that as such a script runs it can be paused by  
pressing Shift-Esc (and then resumed the same way) or aborted by  
pressing Esc.
	b) "pause" which will suspend script execution until any key other  
than Esc or End is pressed.  Pressing End will abort a "paused" script.
	I will be opening a feature-request ticket in our bug database for  
storing some information on a per-frame basis and getting Thermal  
Ellipsoids to use it, with you on the recipient list so that you'll be  
notified when it gets worked on.

> In any case I find Chimera wonderful software that I came upon only
> recently. Thanks guys for developing it!

Thanks!  We're working on our NIH grant renewal right now.  Hopefully  
that will translate into several more years of funding.  Keep your  
fingers crossed!


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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