[Chimera-users] Question about vop maximum

[Reyhan Muhammad]

Thank you Tom for your help.

I followed your suggestion, and indeed the 'extra' densities outside the
vop map are quite small (green map in the attached file). Since you
mentioned about what Chimera does to aligned maps, I then tried to do vop
maximum with unaligned maps.. and they fit perfectly (gray map). Thank you
again.

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On Fri, May 8, 2020 at 6:01 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Reyhan,
>
>   That is a bit mysterious.  Here is a guess.  The pink part outside your
> maximum green map is very small.  You might get a better sense for how well
> the surfaces match by changing all the non-green ones to mesh style.  Since
> you aligned the different maps and then did the "vop maximum #0-5" the new
> maximum map the 6 input maps all have different grid point positions, and
> the new maximum map will use the grid of the first specified map (#0) and
> interpolate (see vop resample docs) the other maps on that grid.  When it
> does the interpolation it averages the 8 nearest grid points (tri-linear
> interpolation).  It may be that that interpolation and your superimposing
> the original maps on the maximum map which have different grid point
> positions is the cause for the slight overlap of the original maps outside
> the maximum when showing contour surfaces.
>
> Tom
>
>
> On May 8, 2020, at 5:40 AM, Reyhan Muhammad <reyhan.muhammad at kaust.edu.sa>
> wrote:
>
> Dear Chimera Users,
>
> I am new to Chimera and cryoEM. For my project, I would like to create a
> single map (which will be used as a mask) for six 3D classes. To achieve
> that, I have aligned all my six maps using Chimera 'Fit in Map' and used
> vop maximum (vop maximum #0,#1,#2,#3,#4,#5) to generate a new map that is
> supposed to 'cover' all the other maps.
>
> My question is, when I look at the vop output map (green map in the file
> attachment), why do we still see some densities from input maps (salmon
> color) outside the vop output map? I have also adjusted the contour level
> of all map to 0.04 (volume all step 1 level 0.04). I hope someone could
> help me to clarify my understanding of vop maximum.
>
> Thank you for your help.
>
> Best wishes,
> Reyhan
>
>
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