[Chimera-users] electron density ven diagram

Tom Goddard goddard at sonic.net
Tue Apr 24 23:10:42 PDT 2012

Hi Terry,

   I used Chimera Python code to intersect two maps, then showed the 
parts of each map lying outside the intersection in mesh in two colors.  
Resulting image and script that produced it is attached.  The 
intersections are smooth because it intersects the original contour 
surfaces instead of masking which produces the jagged artifacts.  If 
your maps are bumpier and more complex then this pair of RNA polymerase 
EM maps I think the image will be too complicated to convey useful 
information.  But for very smooth simple maps it might have some value.

   The surface intersection step is done in Python in the script because 
there is no command to do it currently.  But I could make the "sop clip" 
command do it so no Python would be needed -- just a plain Chimera 
command script.  Currently the "sop clip" command only clips surfaces to 


> Hi Terry,
>   Here's an example although the result isn't pretty.
> open emdbID:1283 emdbID:1284
> volume #0,1 level .35
> mask #0 #1 invert true
> mask #1 #0 invert true
> mask #0 #1
> volume #4 color salmon
> An image of the result is attached vdiff.jpg with gray for parts in 
> map A and not map B, yellow for parts in B and not in A, and red for 
> parts in both.  Here's an explanation of the commands.  The first two 
> just open the maps and set the contour level.  The first mask command 
> produces a new volume equal to map A but with zeros at grid points 
> inside the surface of map B.  The second mask command produces a 
> volume equal to B except 0 inside the surface of A.  The third mask 
> command makes a map equal to A but zero outside the surface of B.  So 
> these new maps are (A not B), (B not A) and (A and B) and are shown as 
> gray, yellow, and red surfaces in vdiff.jpg.  Why does it look so 
> jagged?  That is the result of setting a map to zero above a threshold 
> and then showing a contour surface at that threshold.  It produces a 
> horrible jagged surface because of the saw-tooth patterns of the zeros 
> and non-zeros at the boundary.  If we could make the grid spacing go 
> to zero the picture would instead look like the second attached image 
> vsup.jpg.  This is just the two original map surfaces.  Notice there 
> is no red (points in side both A and B).  At every point on the two 
> surfaces either one surface or the other is on top.  So the only place 
> you see both A and B is on the curved lines where the two surfaces 
> intersect.  The reason you see a lot of red with the above commands is 
> because the grid spacing is actually larger than the separation 
> between the two map surfaces at many points.  It is basically an 
> artifact of discretization.  So to see all 3 components (A not B), (B 
> not A) and (A and B) you'd need to make the first two components 
> transparent.  I've done that in the third attached image vtransp.jpg.  
> It shows the original two maps transparent and the (A and B) red map 
> opaque.  This uses Chimera 1.6 where the default transparency mode is 
> "one transparent layer" so only the gray or yellow top-most 
> transparent layer is shown.  Still it looks like a mess.
> I haven't followed your plan #1 or #2 in detail.  Note that you would 
> need a resulting map with 4 distinct values not 3, with the 4th being 
> points outside both maps.
> My main point is that it is hard to make a useful 3-d Venn diagram 
> since the (A and B) component will be occluded by (A not B) and (B not 
> A).  If the red surface in the last image were smooth it would be a 
> bit better but still hard to visually comprehend.  I have a way to 
> make the red surface smooth (basically just show the part of surface A 
> that lies inside B and part of surface B that lies inside A using 
> original smooth surfaces) but it is not accessible from the Chimera 
> user interface.
>     Tom
>> Hey Guys,
>>         I am interested in making kind of a ven diagram between two 
>> maps for electron density (see attached).  What I would like to do is 
>> where the density is above a certain threshold for both maps, color 
>> the map grey, and where it is above the threshold for map A only, 
>> color red, and for map B only, blue.
>> Plan #1
>> --superimpose maps (have this working)
>> --create a third map (have this working)
>> --do a direct < > = point-by-point comparison between map A and B and 
>> reset the values of the third map to be -1 (map A only), 0 (both 
>> maps) or 1 (map B only)
>> --color the map using the histograms
>> PROBLEM:  The maps are not gridded the same.  After some careful 
>> thought, I don't think I actually can get them gridded the same for 
>> technical reasons.
>> Plan #2
>> --superimpose maps (have this working)
>> --create copy of map A (coarser map) with map A gridding (have this 
>> working)
>> --use interpolation function to interpolate map B (finer map) onto 
>> map A gridding
>> --create copy of map A and do a direct < > = point-by-point 
>> comparison between map A and interpolated map B and reset the values 
>> of the fourth map to be -1 (map A only), 0 (both maps) or 1 (map B only)
>> --color the map using the histograms
>> QUESTION:  Is there an easier way to do this with tools that already 
>> exist in Chimera?  If not, can I get a little bit of info on how the 
>> data is stored in the ccp4 style maps (eg start at origin and loop 
>> over x, loop over y, loop over z or something else?)
>> Let me know if you need more details or clarification on this rats nest.
>> Thanks!
>> Terry

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