[Chimera-users] using chimera on 3D EM map

Weimin Wu wu49 at purdue.edu
Thu Mar 6 11:21:31 PST 2008

Tom Goddard wrote:
> Hi Weimin,
>  Thanks for explaining these problems.  We intend to solve all of them 
> (though it will take some time) and perhaps some already have solutions.
>  1) Volume eraser ball can't be made small enough.  The ball can have 
> any floating point radius value > 0.  So you should be able to make it 
> as small as you like.  I've tried and had no trouble making it tiny.  
> A radius value of 0 is not valid and the ball radius will be left at 
> whatever it was prior to attempting to set it to zero.
>  2) There is no "undo" in volume eraser.  Yes.  This is a serious 
> problem we plan on fixing.
>  3) No way to add density (as opposed to subtracting with volume 
> eraser).  I guess you mean you would like to use a 3d ball to mark the 
> density you wish to keep instead of the density you want to erase.  It 
> might be easy to make a tool like this where you can paint the volume 
> using a ball (like volume eraser).  You could paint using one or more 
> colors and then separate the different colored pieces into separate 
> maps.  The underlying code to do this is already in Chimera (color 
> zone tool, and split map by color zone).  It requires a way to place a 
> marker that matches the painting ball -- basically just a "Color" 
> button on the volume eraser dialog.  Might be able to add this soon.  
> I recently added plane by plane loop drawing for hand tracing surfaces 
> that can be used with the new "mask" command to segment out the 
> enclosed region (in current daily builds).  But from what you say that 
> is less useful in your high resolution case.
>  4) Statistical comparison of two maps.  Chimera can report the 
> correlation coefficient between two maps and it can optimize the 
> position of one map within another.  This tools was called "Fit Map in 
> Map" in the current Chimera production release (version 1.2470) and is 
> called "Fit in Map" (which also handles fitting models) in current 
> Chimera daily builds.  There is also a new option in "Fit in Map" that 
> will update the correlation coefficient in real time as you move one 
> map within the second map.  Also there is a new "Fit in Map" option 
> that will compute a simulated map from a PDB at a given resolution 
> (like EMAN pdb2mrc) and will fit the simulated map and report its 
> correlation in the experimental map.  Are there other measures besides 
> correlation coefficient that you want?  From your example, maybe you 
> want rotations in degrees between two different fits?
>    Tom

Thanks for your reply. I will try the eraser ball again. To add the 
density, I really need something like 3D brush. I have tried a series of 
Markers and split by colors, however it is hard to choose marker 
position and choose color zone radius, because we need separate the 
signals within 4A distance, especially when two subunits cross over and 
one beta sheet is very close to the beta sheet on the other subunit. For 
statistical comparison of two maps, I need not only correlation, but 
also rotation degrees, translation, especially for the hinge region, 
something like rmsd in pdb comparison.


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