[Chimera-users] Difference mapping

Tom Goddard goddard at sonic.net
Wed Mar 2 12:09:49 PST 2016

Hi Saumya,

  The sigmaFactor parameter of the Chimera molmap command that you use to compute the map from your PDB model determines how the resolution value in interpreted by molmap.  I’m not sure what the right value is for what you call FSC gold standard.

	 <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

Although this could probably be figured out from theory.  I think it might be more reliable to simply try several resolutions for the simulated map, take the difference with the experimental map and see what gives the small residuals (SD from menu Tools / Volume Data / Volume mean, sd, and rms).  While you are at it you might also try a few close by pixel sizes for the experimental map to see what gives the smallest residuals.


> On Mar 2, 2016, at 8:45 AM, Saumya Verma  wrote:
> Hello everyone!
> I am relatively new to cryoEM and am solving my first structure. I have a
> question about difference mapping using Chimera, and I’d like to apologize
> in advance if it’s too naïve a question for this forum.
> I have a cryoEM structure of a mutant virus; the x-ray structure of the
> wild-type virus is known. To see the differences between the two
> structures, I am following the following steps:
> - Deleting the mutated chains from the pdb (so that I’ll be able to detect
> these in the cryoEM map) and converting the crystal structure .pdb file to
> .mrc, low pass filtering it to the resolution of the cryo-em refined
> structure and matching box size and A/pix
> - Fitting the two maps in Chimera and subtracting the volumes (using the
> command vop subtract)
> My question is - how do we decide the resolution to which to lowpass
> filter the original structure?
> The reason I’m asking is because while my cryoEM structure is 13.3A (FSC
> gold standard) (I’ve also checked with ResMap – majority of the voxels are
> ~14A), it looks very less detailed when compared to the lowpass-filtered
> map of the original pdb. And when I’m fitting the two, there are major
> differences in the contours, which I think is giving me false differences.
> Can someone please let me know what would be the best way to compare the
> cryoEM structure of mutant virus with the published structure of the
> wild-type virus.
> Thank you very much.
> Regards,
> Saumya
> PhD Student
> Indian Institute of Technology Delhi, India
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