[Chimera-users] View scale and brix output
pett at cgl.ucsf.edu
Wed Mar 7 12:48:20 PST 2007
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
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 at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 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?
> 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:
>> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
>> UCSF Computer Graphics Lab and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> Christopher Akey wrote:
>>> 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
>>> at these maps, but not so good as Chimera for figure making
>>> obviously....then in Chimera we may continue to trim or segment a
>>> and then we want to take it back out, presumably as an MRC file, to
>>> 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
>>> forth using the best of both programs.
>>> cheers C Akey
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
> cheers C Akey
> STRUCTURAL ELECTRON MICROSCOPY & CRYSTALLOGRAPHY GROUP
> Christopher W. Akey, Professor
> Physiology & Biophysics
> Boston Univ. School of Medicine
> 700 Albany St.
> Boston, Mass. 02118-2526
> off: 617 638 4051 lab: 617 638 4088
> fax: 617 638 4041
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