Hello, After looking through the Chimera documentation and examples, I couldn't find any mention of working with volumes. Is that data currently accessible through the API? Thanks, Jonathan Rodgers
Hi Jonathan, All of the Chimera volume data functionality is available using the Python language. We don't have much documentation of Chimera programming interfaces, and it is especially lacking for volumes. The best starting point is probably the example Python scripts page: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts The most important Chimera volume object Python code is in chimera/share/VolumeViewer/volume.py and chimera/share/VolumeData/griddata.py If you describe what you want to program, I can give you more specific pointers. Tom
Hello, After looking through the Chimera documentation and examples, I couldn't find any mention of working with volumes. Is that data currently accessible through the API?
Thanks, Jonathan Rodgers
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hello all, Is it possible to create Chimera movie (MD trajectory animation) with simulation time labeled on the corner ? (Of course after I provide through some appropriate dialogue the time interval between two consequent frames). Thanks in advance for any hint ! Best wishes, Marek
Hello Marek, It may be possible using per-frame scripting in MD Movie (in that tool's menu: Per-Frame... Define script). I've definitely shown frame number as a label for a trajectory, details below. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame> The process would be something like: - figure out equation to convert frame number to time - per-frame script would use that equation and show result as a 2D label - record movie while the per-frame script is active I think it would be necessary to do it in Python, to include the equation part, but the script dialog provides a way to use frame number in the script. The only part I am concerned about is whether the equation output (simulation time) has to be converted to a character string to be used as label contents. I have definitely used this process to simply show the frame number as a label during the trajectory. That is done with a per-frame script of Chimera commands in the "Trajectory and Ensemble Analysis" tutorial, part 1: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 15, 2011, at 9:37 AM, Marek Maly wrote:
Hello all, Is it possible to create Chimera movie (MD trajectory animation) with simulation time labeled on the corner ? (Of course after I provide through some appropriate dialogue the time interval between two consequent frames). Thanks in advance for any hint ! Best wishes, Marek
Hello Elaine, thanks a lot for prompt and useful advice ! Best wishes, Marek Dne Wed, 15 Jun 2011 19:08:38 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hello Marek, It may be possible using per-frame scripting in MD Movie (in that tool's menu: Per-Frame... Define script). I've definitely shown frame number as a label for a trajectory, details below.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
The process would be something like: - figure out equation to convert frame number to time - per-frame script would use that equation and show result as a 2D label - record movie while the per-frame script is active
I think it would be necessary to do it in Python, to include the equation part, but the script dialog provides a way to use frame number in the script. The only part I am concerned about is whether the equation output (simulation time) has to be converted to a character string to be used as label contents.
I have definitely used this process to simply show the frame number as a label during the trajectory. That is done with a per-frame script of Chimera commands in the "Trajectory and Ensemble Analysis" tutorial, part 1: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 15, 2011, at 9:37 AM, Marek Maly wrote:
Hello all, Is it possible to create Chimera movie (MD trajectory animation) with simulation time labeled on the corner ? (Of course after I provide through some appropriate dialogue the time interval between two consequent frames). Thanks in advance for any hint ! Best wishes, Marek
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
To expand a little on the details, I think that outside the trajectory script you would create a 2D label for the script to work with, something like: 2dlabels create timer text "0 ns" which would create a label that can be referred to with the name "timer" in subsequent commands. Then just use the 2D Labels tool to position, color, and size the label as you like. Then your trajectory script would be something like: from chimera import runCommand runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame'] * 27.5)) The '%.1f' part means show a floating point number with one decimal place. You can change the label text surrounding that as appropriate. Change 27.5 to whatever conversion factor is appropriate, possibly adding an offset if your time doesn't start at zero. --Eric On Jun 15, 2011, at 10:08 AM, Elaine Meng wrote:
Hello Marek, It may be possible using per-frame scripting in MD Movie (in that tool's menu: Per-Frame... Define script). I've definitely shown frame number as a label for a trajectory, details below.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.ht...
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#pe...
The process would be something like: - figure out equation to convert frame number to time - per-frame script would use that equation and show result as a 2D label - record movie while the per-frame script is active
I think it would be necessary to do it in Python, to include the equation part, but the script dialog provides a way to use frame number in the script. The only part I am concerned about is whether the equation output (simulation time) has to be converted to a character string to be used as label contents.
I have definitely used this process to simply show the frame number as a label during the trajectory. That is done with a per-frame script of Chimera commands in the "Trajectory and Ensemble Analysis" tutorial, part 1: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 15, 2011, at 9:37 AM, Marek Maly wrote:
Hello all, Is it possible to create Chimera movie (MD trajectory animation) with simulation time labeled on the corner ? (Of course after I provide through some appropriate dialogue the time interval between two consequent frames). Thanks in advance for any hint ! Best wishes, Marek
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Eric, thanks a lot for providing all the necessary details ! Best wishes, Marek Dne Wed, 15 Jun 2011 19:44:19 +0200 Eric Pettersen <pett@cgl.ucsf.edu> napsal/-a:
To expand a little on the details, I think that outside the trajectory script you would create a 2D label for the script to work with, something like:
2dlabels create timer text "0 ns"
which would create a label that can be referred to with the name "timer" in subsequent commands. Then just use the 2D Labels tool to position, color, and size the label as you like. Then your trajectory script would be something like:
from chimera import runCommand runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame'] * 27.5))
The '%.1f' part means show a floating point number with one decimal place. You can change the label text surrounding that as appropriate. Change 27.5 to whatever conversion factor is appropriate, possibly adding an offset if your time doesn't start at zero.
--Eric
On Jun 15, 2011, at 10:08 AM, Elaine Meng wrote:
Hello Marek, It may be possible using per-frame scripting in MD Movie (in that tool's menu: Per-Frame... Define script). I've definitely shown frame number as a label for a trajectory, details below.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
The process would be something like: - figure out equation to convert frame number to time - per-frame script would use that equation and show result as a 2D label - record movie while the per-frame script is active
I think it would be necessary to do it in Python, to include the equation part, but the script dialog provides a way to use frame number in the script. The only part I am concerned about is whether the equation output (simulation time) has to be converted to a character string to be used as label contents.
I have definitely used this process to simply show the frame number as a label during the trajectory. That is done with a per-frame script of Chimera commands in the "Trajectory and Ensemble Analysis" tutorial, part 1: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 15, 2011, at 9:37 AM, Marek Maly wrote:
Hello all, Is it possible to create Chimera movie (MD trajectory animation) with simulation time labeled on the corner ? (Of course after I provide through some appropriate dialogue the time interval between two consequent frames). Thanks in advance for any hint ! Best wishes, Marek
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
On Jun 15, 2011, at 10:44 AM, Eric Pettersen wrote:
from chimera import runCommand runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame'] * 27.5))
This was so close to being correct. :-( Since frame numbers start at 1, the last part needs to be: % ((mdInfo['frame']-1) * 27.5)) --Eric
OK, thanks a lot ! Best, Marek Dne Wed, 15 Jun 2011 19:50:04 +0200 Eric Pettersen <pett@cgl.ucsf.edu> napsal/-a:
On Jun 15, 2011, at 10:44 AM, Eric Pettersen wrote:
from chimera import runCommand runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame'] * 27.5))
This was so close to being correct. :-( Since frame numbers start at 1, the last part needs to be:
% ((mdInfo['frame']-1) * 27.5))
--Eric
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
participants (5)
-
Elaine Meng -
Eric Pettersen -
Jonathan Rodgers -
Marek Maly -
Tom Goddard