how to reduce EM map resolution (Chimera 1.6.2)
Hello I have low-resolution (~15A) model of decorated F-actin. I want to localize the "decoration" element by subtracting normal F-actin model obtained from Cryo-EM (EMD-5168) from my decorated model. The problem is that EMD-5168 has a higher resolution and "vop" command did not work. Even if it would work, it would be difficult to interpret the result of such subtraction. I think, both maps should be at approximately the same resolution. I know how to create low-resolution map from PDB, but I could not find any solution how to lower the resolution of the EMD-5168.map Any help would be greatly appreciated. Many thanks in advance. Sergey -- ____________________________________________________________________ Sergey Ryazantsev Ph. D. Electron Microscopy Laboratory (EMi) Department of Biological Chemistry, David Geffen School of Medicine University of California, Los Angeles. Phone: (310) 825-1144 (office) mailto:sryazant@ucla.edu
Hi Sergey, You can lower the resolution of the EMDB 5168 (6.6 Angstrom) F-actin map by Gaussian filtering open #0 emdbID:5168 vop gaussian #0 sdev 5 model #1 This will create a new map by convolution with a Gaussian that has 5 A standard deviation. Then you can subtract this map from your map. open #2 mymap.mrc vop subtract #2 #1 minRMS true model #3 Here the "minRMS true" option says to scale the second map to minimize the residual (sum of squares over grid points above second map threshold level). This handles the different normalizations of the two maps. What standard deviation should you use in the Gaussian smoothing? I suggest trying different values and see which one gives the smallest residuals. The different definitions of "resolution" used in EM make it hard to predict the exact standard deviation you will need to match the two maps. I also noticed that 5168 has some kind of cylindrical noise artifacts if you go to lower threshold levels. These appear in the smoothed version of that map as a solid cylindrical shell at low threshold level. Perhaps the level of that artifact is low enough that it won't bother you in your difference map. But if it does you may need to mask it out with the Chimera "mask" command and "shape cylinder" command. Tom -------- Original Message -------- Subject: [Chimera-users] how to reduce EM map resolution (Chimera 1.6.2) From: Sergey Ryazantsev To: chimera-users@cgl.ucsf.edu Date: 2/11/13 8:02 PM
Hello I have low-resolution (~15A) model of decorated F-actin. I want to localize the "decoration" element by subtracting normal F-actin model obtained from Cryo-EM (EMD-5168) from my decorated model. The problem is that EMD-5168 has a higher resolution and "vop" command did not work. Even if it would work, it would be difficult to interpret the result of such subtraction. I think, both maps should be at approximately the same resolution. I know how to create low-resolution map from PDB, but I could not find any solution how to lower the resolution of the EMD-5168.map
Any help would be greatly appreciated. Many thanks in advance. Sergey
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Sergey Ryazantsev -
Tom Goddard