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Hi Jin,
SFTOOLS doesn't get a lot of use/testing for working with maps and it's
a long time I ago that I wrote that code but you may give the following
a try, no promises thought :)
##Attempt to make the map span the full unit cell
sftools
mapin oldEM.map
maplimit fract 0 1 0 1 0 1
mapout newEM.map
exit
## Attempt to calculate structure factors directly. Don't remember if
## spacegroup and cell are part of the map header so you may not need
## the first 4 lines
sftools
set spacegroup
P1
set cell
a b c alpha beta gamma (use whatever values EM suggests)
mapin EM.map
map2sf col Fmap Pmap
write EMmap.mtz
exit
The latter should create two columns named Fmap and Pmap with the
amplitudes and phases from map inversion. You can also set the
resolution to which the structure factors will be calculated.
use COMMAND HELP on any command to get online help.
Bart
Jin K. Yang wrote:
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Hi all,
I'm trying to get Fc from EM map for the use of MR search model.
The EM map is now in the P1 cell which has 64 grid points on each axes, and is
in the box [-32 to 31, -32 to 31, -32 to 31].
When I tried SFALL to get Fc from this map, the SFALL compained as below in the
last part of the logfile.
Check map header agrees with fixed requirements for SFcalc for this
spacegroup.
Check KV1 KV2 KU1 KU2 Ksec,Msec - IXmin IXmax..
-32 31 -32 31 -32 64 0 63 0 63 0 63
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
SFALL: **** Fatal disagreement between input info and map header
It looks to me that my map should be located in the [0 63, 0 63, 0 63] which is
an asu defined in SFALL.
The manual of SFALL also looks like indicating this point.
The EM density has a shape of a triangular disk whose center is located in the
origin of the coordiates system.
How can I move this density into the box [0 63, 0 63, 0 63] and update map
header information accordingly so that SFALL can read my density ?
Thanks in advance.
JK
--
==============================================================================
Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
==============================================================================
