More anecdote - with a GP3 structure we took the EM map generated by the
electron microscopists - fortunately available in CCP4 format, and
generated SFS from it using SFALL ( This can now be done within MOLREP I
believe)
There are some issues to think about. At least in the EM map we were
given the scale and the ZERO level were both a bit out.
I had to rescale the maps by factors from 0.95 to 1.05; I did that by
just editing the CELL card. manually - you can run maptona4 to get an
ASCII version of the map; edit the cell , then convert the map back.
There must be a more elegant way, but that worked.
It was much harder to change the zero level. Within the map there are
empty areas, flagged by the grid points being set to 0.000, and areas
which fit the molecule, which can range from -2 say to 20.
If you add a factor to the map using mapmask, then the empty areas are
also reset from 0.00. I had to make a mask from the original map, reset
the values then remask the points.
The good news is that EM experts say that they are getting much better
at getting the EM scale correct..
Eleanor
Randy J. Read wrote:
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On Jun 8 2006, [EMAIL PROTECTED] wrote:
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Dear All:
I know it is possible to use EM map for model of molecular
replacement. I wonder if anyone can tell me how exactly to do it. I
have a 10 A EM map and 3 A X-ray data. I can convert EM map (ccp4
format) into mtz file by using mapman and sFALL. Which software I
should use to do molecular replacement and how to set its parameters.
After getting the solution from the molecular replacement, how do I
extend the phase?
Further to Martyn's comment, we have a web page that addresses some of
the issues of using electron density as a model for Phaser, at
http://www-structmed.cimr.cam.ac.uk/phaser/density_as_model.html. It
deals specifically with the case of cutting out density from a
crystallographic map, but many of the considerations are the same for
using EM density.
As for extending the phases, that's going to depend on whether or not
you have lots of non-crystallographic symmetry. If not, the EM model
would probably be most useful for finding substructures for
experimental phasing.
Randy Read
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