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

Tom Goddard goddard at cgl.ucsf.edu
Thu Mar 6 10:00:01 PST 2008

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?


Weimin Wu wrote:
> Dear Prof.:
> I am one postdoctoral in Prof. Wenjiang's group. We have employed 
> Chimera in our research and really appreciate it. However when our 3D 
> map goes beyond 5A (see Feb. 28, 2008 Nature paper) which enabled us 
> to see the boundaries among alpha helices and beta sheets, we meet 
> some problems in the segmentation which we do think you could help us 
> out.
> One problem is that the viewer eraser ball is too big even the radius 
> is set to zero. It prevented us from completely clearing the 
> neighboring signals. There is no undo option when using the eraser 
> function. Therefore we have to keep saving the intermediate maps.
> Another problem is that there is no 3D volume editor which can let us 
> add density in 3D EM map. Sometimes this is the most important for the 
> segmentation, because it is hard to tell which density should be 
> included if we go slice by slice, but it is much easier to tell 
> directly in 3D map with the stereo function.
> Another problem is that there is no statistical tool for analyzing the 
> slight difference between two 3D EM maps. Therefore it makes hard to 
> determine the fit quality of one map into the other, for example, when 
> fitting one subunit into the other, there is some conformation 
> difference between them, but we need quantitative values to evaluate 
> the difference and make a story. Something like in two PDBs, we can 
> fit one domain and check the difference of the other domain.
> If I don't explain the problems clearly, please let me know. Many thanks,
> weimin wu

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