[Chimera-users] Difference mapping
blz108038 at bioschool.iitd.ac.in
Wed Mar 2 08:45:23 PST 2016
I am relatively new to cryoEM and am solving my first structure. I have a
question about difference mapping using Chimera, and Id like to apologize
in advance if its 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 Ill 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 Im asking is because while my cryoEM structure is 13.3A (FSC
gold standard) (Ive 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 Im 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
Thank you very much.
Indian Institute of Technology Delhi, India
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