Just to clarify some of the things that Elaine was unsure of: if a model gets closed that was involved in saved positions then it will simply be ignored when the position is restored. If some new model gets the same ID and sub-ID # as the closed model then that model will be positioned as if it were the closed model (except for per-model clip planes). --Eric On Mar 7, 2007, at 12:24 PM, Elaine Meng wrote:
Hi Christopher, As long as you save the session after using savepos the positions should be there. However, as you suspected the model numbers are important - the individual transformations for the models are restored based on those model numbers. I think it will restore the positions of whichever models are there, despite complaining that some are missing (it's been a while, I'd have to try it to make sure). If you closed model 0 and opened a new model 0 it might try to put it in the position the old model 0 was in. Also not sure about that one. When I use saved positions for my own work, I don't delete/add models between saving and restoring the positions.
I can't really envision how positions could be saved without using the model numbers. The only other thing I can think of is data file name, but frequently one will have the same data file opened as more than one model at a time, with different transformations. ----- 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 Mar 7, 2007, at 12:15 PM, Christopher Akey wrote:
Elaine -
yeah,that does seem to work nicely within a session, lets see what happens when I close and reopen it. However, is the savepos option sensitive to things like deleting one object from the session before closing, then opening and adding a new object (now the numbering of the objects may vary and this seems to screw up matrices that are saved cause they depend on the numbers). I would hope that savepos doesn't depend on numbered objects?
cwa
Meng wrote:
Hi Christopher, Tom did mention "reset," but I thought I'd expand on that topic a bit. You can actually save multiple named positions, which will then be included in a single saved session. When I make a set of figures that differ in view and scale but with basically the same display/coloring setup, I use the "savepos" command to save the position for each figure, and then save the session. It doesn't matter what position everything is in when you save the session, because you will still be able to get back to any of those saved positions with "reset." The saved positions include scale. If you really only want to restore scale, currently you could note the value shown in the Camera tool (as mentioned by Tom), and later type that into the Camera tool to restore it. more about savepos and reset: http://www.cgl.ucsf.edu/chimera/1.2304/docs/UsersGuide/midas/ savepos.html http://www.cgl.ucsf.edu/chimera/1.2304/docs/UsersGuide/midas/ reset.html 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 Christopher Akey wrote:
Tom-
A few more issues that have come up for user friendliness.
1. It would be useful to have a box where the user can specify the absolute scale for the session, the first time it is opened, this could be set at 1.0 for example after loading a ribosome map and the atomics and putting them to a good size.
Then the program should keep track of the changes made during the session using the scale command (I guess you can't track changes made with the mouse so one generally would avoid this, or even better one should be able to turn off the mouse scale feature!).
This way one could always look at the pull down for the current scale value when you capture a particular view for a figure.
One could then return to the original scale of 1.0 at the end of session or write down the current scale value, which could be kept in the ssesion. So upon reopening the session at a later date, one can always get back to the correct scale to recapture a panel for a figure. This is currently a real problem, as far as I can tell.
2. We often want to import a brix file with aligned pdbs, since we dock and look at them in 'O', which is better in some ways for looking at these maps, but not so good as Chimera for figure making obviously....then in Chimera we may continue to trim or segment a map, and then we want to take it back out, presumably as an MRC file, to be converted into a brix by a conversion program (for us its SPIDER). Then one can do another cycle of docking in 'O' using the refined/cleaned up sub map from Chimera.
While I can think of one way to do this without losing the relative origins and thus, the map alignments, it is pretty tedious. If one could write the zoned or volume erased brix volume back out as a new brix file, with the correct dimensions and origin, relative to the brix file brought into Chimera, this would allow you to cycle back and forth using the best of both programs.
cheers C Akey
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-- cheers C Akey
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