Hi Melanie,
Mapmask was suggested. The XYZLIM command of mapmask takes values in grid
points or fractional coordinates.
You could make a 300A cube by giving fractional coordinates of 300/(current
cell edge),
But since that doesn't change the grid it won't change the thickness of your
slices.
I don't think mapmask (old name "extend") can change the grid.
Maprot was also mentioned, and I think this should work. You need to generate a
300x300x300 target map (WORKIN) and perhaps a mask (could be your entire
current cell). Use the identity rot-trans operator, or with some non-zero
translation if necessary to get your model entirely in one cell.
But it might be much easier to just recalculate your map from structure factors
with equal grid spacings using fft.
So if you want half-angstrom slices, set the grid values (nx,ny,nz) to twice
the cell dimensions in Angstroms.
The FFT has some restrictions on the grid so you may not be able to choose
exactly what you want, but could get pretty close to even spacing. (In fact
programs that write maps tend to make approximately equal spacing, like 1/2 or
1/3 of the resolution, by default- so it would be surprising if your current
map has drastically different spacing along the different axes). If you expand
your data to P1 before fft, then the only restrictions are that nz be an even
number (and none of the nx,ny,nz have prime factors greater than 19). You
should be able to get very nearly equal spacing with that.
I wonder if there is any program that uses conventional FT and allows arbitrary
grid choices?
eab
On 07/16/2018 11:28 AM, melanie.voll...@diamond.ac.uk wrote:
Thanks everyone who replied to my post. I got a wealth of ideas.
Melanie
Hello everyone,
I have a question about manipulating map files.
I want to use my map derived from X-ray diffraction and create a standard
volume for it, say 300A3.
This is to be able to create slices of equal dimensions along all three
directions of the electron density stored in the map file. Currently my slices
differ in dimensions as the default volume is defined by the unit cell.
I don't think there is anything in the map tools from the X-ray field I know. I
had a play with Chimera and I think there is a tool in there to use some form
of reference cell created from coordinates. But I don't want to make use of a
coordinates file.
I just want to inflate my unit cell to a standard volume.
Any ideas would be very welcome.
Thanks
Melanie
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