Hi,
I am writing a movie script that uses the vop morph command to morph between two EM maps #0 and #1:
vop morph #0,1
The output map #2 from this command is displayed in a random default color that I would like to change. I have tried the following:
vop morph #0,1 volume #2 color khaki
This works, but the very first frame in the movie following the vop morph still contains the default color, while the following frames contain the set color 'khaki'. This results in a flicker in the movie with the wrong color. Any help/suggestions on how to get this set correctly? Let me know if there needs clarification - thanks!
I am using Chimera Version 1.6 Mac OSX
Hi Steve, To avoid displaying intermediate states, you can combine commands on one line with semicolon separators, for example:
vop morph #0,1; volume #2 color khaki
See the general information on command files: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile
Another possibility in this case is to create the morph volume, color it as desired, and hide it before starting recording (before the "movie record" command), and just redisplay it later in the movie content portion of the script.
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 Feb 28, 2013, at 8:20 AM, Steve Reichow wrote:
Hi, I am writing a movie script that uses the vop morph command to morph between two EM maps #0 and #1:
vop morph #0,1
The output map #2 from this command is displayed in a random default color that I would like to change. I have tried the following:
vop morph #0,1 volume #2 color khaki
This works, but the very first frame in the movie following the vop morph still contains the default color, while the following frames contain the set color 'khaki'. This results in a flicker in the movie with the wrong color. Any help/suggestions on how to get this set correctly? Let me know if there needs clarification - thanks!
I am using Chimera Version 1.6 Mac OSX
Thank you Elaine! In this case the first suggestion, using a semi-colon separator worked perfectly. Thanks again!
On Thu, Feb 28, 2013 at 12:25 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Steve, To avoid displaying intermediate states, you can combine commands on one line with semicolon separators, for example:
vop morph #0,1; volume #2 color khaki
See the general information on command files: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile
Another possibility in this case is to create the morph volume, color it as desired, and hide it before starting recording (before the "movie record" command), and just redisplay it later in the movie content portion of the script.
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 Feb 28, 2013, at 8:20 AM, Steve Reichow wrote:
Hi, I am writing a movie script that uses the vop morph command to morph
between two EM maps #0 and #1:
vop morph #0,1
The output map #2 from this command is displayed in a random default
color that I would like to change. I have tried the following:
vop morph #0,1 volume #2 color khaki
This works, but the very first frame in the movie following the vop
morph still contains the default color, while the following frames contain the set color 'khaki'. This results in a flicker in the movie with the wrong color. Any help/suggestions on how to get this set correctly? Let me know if there needs clarification - thanks!
I am using Chimera Version 1.6 Mac OSX
Hi, Is it possible to generate a morphing between two volumes in Chimera, if the volumes have slighly different sizes, e.g. 100x100x100 vs. 101x101x101 pixels? Can I crop or pad a volume in Chimera?
Thanks, Henning.
On Feb 28, 2013, at 6:25 PM, Elaine Meng wrote:
Hi Steve, To avoid displaying intermediate states, you can combine commands on one line with semicolon separators, for example:
vop morph #0,1; volume #2 color khaki
See the general information on command files: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile
Another possibility in this case is to create the morph volume, color it as desired, and hide it before starting recording (before the "movie record" command), and just redisplay it later in the movie content portion of the script.
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 Feb 28, 2013, at 8:20 AM, Steve Reichow wrote:
Hi, I am writing a movie script that uses the vop morph command to morph between two EM maps #0 and #1:
vop morph #0,1
The output map #2 from this command is displayed in a random default color that I would like to change. I have tried the following:
vop morph #0,1 volume #2 color khaki
This works, but the very first frame in the movie following the vop morph still contains the default color, while the following frames contain the set color 'khaki'. This results in a flicker in the movie with the wrong color. Any help/suggestions on how to get this set correctly? Let me know if there needs clarification - thanks!
I am using Chimera Version 1.6 Mac OSX
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Henning, I believe map morphing requires the input maps to have the same grids, but you can resample a map onto the grid of another (making a new map that is congruent with the second) using command "vop resample": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample
That's probably the best approach if the main purpose is to get the same grid so that you can do morphing.
More generally, cropping and writing out the cropped region can be done using the Volume Viewer tool (see Features menu "Region bounds" and/or "Subregion selection" and File menu "Save Map as...") http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#features http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#organization
... or the corresponding options of the"volume" command http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html
For general zero-padding, I guess it could be done with "vop cover" although that is not the command's main purpose. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover
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 Feb 28, 2013, at 12:41 PM, Henning Stahlberg wrote:
Hi, Is it possible to generate a morphing between two volumes in Chimera, if the volumes have slighly different sizes, e.g. 100x100x100 vs. 101x101x101 pixels? Can I crop or pad a volume in Chimera? Thanks, Henning.
Hi Henning,
Morph map just does a linear interpolation between corresponding map grid points and it requires the map sizes be the same. Also the grids of the two maps should exactly match if you want sensible results. If your maps are different sizes or the same size but the grids are not aligned you would use the "vop resample" command to interpolate one map on the grid of the other. For example,
vop resample #1 ongrid #0 model #2 vop morph #0,2
I've intended for a long time to make morph do the trilinear interpolation automatically (as done by "vop resample") if the grids didn't align or have matching sizes but have not gotten to that.
http://plato.cgl.ucsf.edu/trac/chimera/ticket/11504
Tom
On Feb 28, 2013, at 12:41 PM, Henning Stahlberg wrote:
Hi, Is it possible to generate a morphing between two volumes in Chimera, if the volumes have slighly different sizes, e.g. 100x100x100 vs. 101x101x101 pixels? Can I crop or pad a volume in Chimera?
Thanks, Henning.
On Feb 28, 2013, at 6:25 PM, Elaine Meng wrote:
Hi Steve, To avoid displaying intermediate states, you can combine commands on one line with semicolon separators, for example:
vop morph #0,1; volume #2 color khaki
See the general information on command files: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile
Another possibility in this case is to create the morph volume, color it as desired, and hide it before starting recording (before the "movie record" command), and just redisplay it later in the movie content portion of the script.
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 Feb 28, 2013, at 8:20 AM, Steve Reichow wrote:
Hi, I am writing a movie script that uses the vop morph command to morph between two EM maps #0 and #1:
vop morph #0,1
The output map #2 from this command is displayed in a random default color that I would like to change. I have tried the following:
vop morph #0,1 volume #2 color khaki
This works, but the very first frame in the movie following the vop morph still contains the default color, while the following frames contain the set color 'khaki'. This results in a flicker in the movie with the wrong color. Any help/suggestions on how to get this set correctly? Let me know if there needs clarification - thanks!
I am using Chimera Version 1.6 Mac OSX
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Elaine Meng -
Henning Stahlberg -
Steve Reichow -
Tom Goddard