Thermal ellipsoids are not updated when playing multi-frame PDB trajectory
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 ?
In any case I find Chimera wonderful software that I came upon only recently. Thanks guys for developing it!
With best regards, Lukasz
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 modeldisp #0.1; some-timing-command ~modeldisp #0.1; modeldisp #0.2; some-timing-command ~modeldisp #0.2; modeldisp #0.3; some-timing-command etc.
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 ".com". 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
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On 03/31/2011 09:48 PM, Eric Pettersen wrote:
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 modeldisp #0.1; some-timing-command ~modeldisp #0.1; modeldisp #0.2; some-timing-command ~modeldisp #0.2; modeldisp #0.3; some-timing-command etc.
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 ".com". A couple of points about the script:
- 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
Dear Eric,
Thanks for your advice and the ticket. At the moment I can live with single frame view, since I only need a few representative snapshots. It would be however very useful to have a dynamic thing as well, so I am looking forward to the follow up from the feature request list.
And I definitely keep my fingers crossed for the grant renewal!
Best regards, Lukasz
participants (2)
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Eric Pettersen -
Lukasz Walewski