[Chimera-users] savepos/reset

Tom Goddard goddard at cgl.ucsf.edu
Mon Dec 8 23:08:14 PST 2008

Hi Matt,

  Yeah, the savepos/reset commands is pretty unfriendly.  I think the 
sensible fix is that "reset" should be changed to move unknown models in 
some sensible way instead of just leaving them where they lie.  The 
common case is that the transformation of all remembered models is the 
same, so position any new model using that same transformation.  If some 
models have different saved transformations then it might be reasonable 
to look just at the models with the same current transformation as the 
new model -- if all those end up with the same transform then apply that 
to the new model as well.  If there is some real ambiguity (models with 
the same current transform match the new model and then move to 
different relative positions in the saved position) then obviously you 
have to specify how to incorporate the new model in that saved 
position.  I won't have time to work on this for probably a few months.  
Perhaps another Chimera developer will look at it.

  As things currently work I think the only approach is quite painful.  
You have to reset to a saved position then use the Model Panel  / Match 
button to align your new model with one of the existing models, then 
reuse the "savepos" command with the original name to augment it.  Ugh.  
The matrixcopy command does the same think as the Match button and may 
be easier.


Matthew Dougherty wrote:
> Let's say I have 5 models and I save a number of positions (savepos).
> Then I later create some morphs between the models.
> When I do a reset of a position, the morph model's position does not  
> correspond with the other model positions.
> This is partially due to the method of camera control in chimera of  
> moving the models and keeping the camera position pointing in the z  
> direction.
> Is there a way to incorporate the morph model into the saved positions  
> that were created prior to the creation of the morph model?
> having similar problem with models I open after the positions are saved.
> thanks, Matt

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