Step 4: Compute 3D density with SFs from XPLOR

Step 4: Compute 3D density with SFs from XPLOR

Overview

a. Change format of structure factor (SF) file with EMFORMAT

i. Compile EMFORMAT if necessary

ii. Run EMFORMAT

iii. In EMFORMAT, enter unit cell size in pixels and unit cell angles in degrees

iv. In EMFORMAT, weight the structure factors if desired

b. Run EMSF3DBT, to invert SFs

Detailed instructions

a. Change SF format to one compatible with EMSF3DBT. It adds a header and other parameters essential to the EMSF3DBT program.

i. The program may need to be compiled. If so, on a UNIX machine execute the command "f77 emformat.f", which gives an executable file named "a.out".

ii. Run program EMFORMAT. Input is fc.xpl. The output is in ASCII format, and the filename is chosen by the user.

iii. In EMFORMAT, you will be asked to enter "a, b, c (in pixels), alpha, beta, gamma (in deg.)". Alpha, beta, and gamma are the same as you used in steps 2 and 3. The unit cell parameters, a, b, and c, are the dimensions of the unit cell in pixels. EMSF3DBT seems to work best if the pixel a, b, and c values are even numbers. The unit cell size you entered in steps 2 and 3 divided by the number you enter here equals the pixel size in Å.

iv. In EMFORMAT, you may weight the SF amplitudes. You should downweight them if the amplitudes are too large for the ASCII-formatted output file.

b. Compute 3D density by running EMSF3DBT