[Chimera-users] View scale and brix output

Eric Pettersen 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
>                      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 at 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
> ------------------------------------------------------------------
> ------------------------------------------------------------------
>   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
>   cakey at bu.edu
>   http://biophysics.bumc.bu.edu/faculty/akey/index.html
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