good morning Tom, there isn't by chance a way to output the orientation/location of a given model (or, likewise, its corresponding per-model clipping plane) so that I can write down particular views that are useful, without having to re-save chimera sessions with unique IDs (my kludge as of right now). and a related follow-up - if so, how do I re-input the orientations by command line in chimera (if possible?) thanks, -jeff
Hi Jeff, The Chimera "savepos <name>" command allows you to save views including clip plane positions. You return to a view with command "reset <name>". The named views are saved in Chimera sessions. So you can just keep one Chimera session with as many named views as you want. The "reset list" command lists all named views. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html Tom
thanks Tom, is there a command to set the per-model clipping plane to intersect an axis (like the x, y, or z axis of a volume map, or the global x, y, or z axis, etc) -j Thomas Goddard wrote:
Hi Jeff,
The Chimera "savepos <name>" command allows you to save views including clip plane positions. You return to a view with command "reset <name>". The named views are saved in Chimera sessions. So you can just keep one Chimera session with as many named views as you want. The "reset list" command lists all named views.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html
Tom
Hi Jeff, There is a button on the Per-Model Clipping dialog that lets you align the plane perpendicular to the screen. There is no other capability for aligning the plane perpendicular to an axis. I sometimes use this button in combination with keyboard shortcuts so (standard orientation), and x9, y9, z9 (rotate about x, y, or z axis by 90 degrees). You turn on keyboard shortcuts using menu entry Tools / General Controls / Accelerators On. I have them turned on by default using the Preferences dialog. With these shortcuts the clip plane can be oriented perpendicular to various axes although it is a bit complicated. Is part of your question that you also want to adjust the position where the plane intersects a given axis -- for example, a slider to move the plane keeping its orientation fixed, and report its position along the axis? It is easy to add all those controls although it would greatly expand the per-model clipping dialog. We would need some user interface that hides some of that complexity for users who do not need it. Tom
Hi Jeff, There isn't a command (unless Tom Goddard has made an accelerator for this), but if I were trying to position the per-model clipping plane normal to a volume data axis I would take this approach: (1) align volume data using the Orient button on Volume Viewer. This will point the axes of the current data set in the standard directions: X horizontal in the plane of the screen increasing rightward, Y vertical in the plane of the screen increasing upward, and Z perpendicular to the screen increasing outward from the screen. (2) depending on which axis you want the per-model clipping plane to be normal to, optionally use the command "turn" to rotate the volume data 90 degrees around some axis (3) use the "Orient plane" button on Per-Model Clipping to place the plane perpendicular to the line of sight, and optionally the "Flip plane" button depending on which side you want to be visible For example, to align the per-model clipping plane normal to the Z axis of the data, you could skip #2 above. To align the per-model clipping plane normal to the X axis of the data, step #2 would be to use the command "turn y 90" or turn y -90" (aligning the data X axis along the laboratory Z axis). A little bit of a brain teaser... I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 16, 2007, at 2:05 PM, Jeff wrote:
thanks Tom,
is there a command to set the per-model clipping plane to intersect an axis (like the x, y, or z axis of a volume map, or the global x, y, or z axis, etc)
-j
Thomas Goddard wrote:
Hi Jeff,
The Chimera "savepos <name>" command allows you to save views including clip plane positions. You return to a view with command "reset <name>". The named views are saved in Chimera sessions. So you can just keep one Chimera session with as many named views as you want. The "reset list" command lists all named views.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html
Tom
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Hi Jeff, Take a look at the commands "matrixget" and "matrixset": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html That can be used for the models, but not the per-model clipping planes. One other thing you might not know is that you can save multiple positions in a single session (i.e. you don't have to save a session for each position). Positions are named/saved with the command "savepos" and reapplied with "reset": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html These positions definitely include the global clipping plane positions. I'm not sure about the per-model clipping plane positions. Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 16, 2007, at 10:57 AM, Jeff wrote:
good morning Tom,
there isn't by chance a way to output the orientation/location of a given model (or, likewise, its corresponding per-model clipping plane) so that I can write down particular views that are useful, without having to re-save chimera sessions with unique IDs (my kludge as of right now). and a related follow-up - if so, how do I re-input the orientations by command line in chimera (if possible?)
thanks,
-jeff
On Jan 19, 2007, at 11:13 AM, Elaine Meng wrote:
One other thing you might not know is that you can save multiple positions in a single session (i.e. you don't have to save a session for each position). Positions are named/saved with the command "savepos" and reapplied with "reset": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/savepos.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html
These positions definitely include the global clipping plane positions. I'm not sure about the per-model clipping plane positions.
They unfortunately do not contain the per-model clip planes yet. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
participants (4)
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Elaine Meng -
Eric Pettersen -
Jeff -
Thomas Goddard