[Chimera-users] segmentation and resolution

Kristin Parent kparent at msu.edu
Fri Sep 23 07:52:47 PDT 2016

To whom it may concern,

I am currently working on segmenting a high resolution cryo-EM map (~4Å by
the ³gold standard FSC²) to phase crystallography data. After the
segmentation, my colleague doing the phasing tells me that map appears more
like 12Å resolution and I am worried I am doing something wrong during the
process and somehow distorting my original data. I believe the 4Å of the
original map based on structural features that I can clearly see. And the
segmented density does not appear as defined. Therefore it appears that
there has been some changes.

In order to begin the process, I did some manipulations before I started.
This is an icosahedral virus map created through Auto3dem. I am only using
an small quadrant of the  original map, and since it was in pif format
originally, I used proc3d to convert to mrc and invert the contrast to be
compatible with segger. Before segmentation the map visually looked the same
as the original pif map when both were displayed in chimera.

The procedure I followed after segmentation was: "Save selected regions to
.mrc file... save density map masked by the selected
segmentation regions to an MRC file (map dimensions set to the minimal box
containing the regions)². I have made sure that the correct binning has been
applied during segmentation.

Any help would be much appreciated. Kristin

Kristin N. Parent, Ph.D.
Assistant Professor
Dept. of Biochemistry and Molecular Biology
Michigan State University
603 Wilson Road
Room 519 Biochemistry Building
East Lansing, MI 48824
Office phone: (517) 432-8434


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