Step 3: Compute structure factors with XPLOR

 

Overview

a. Edit script file fcalc.inp

i. Enter unit cell values

ii. Set resolution

iii. Enter filename for non-crystallographic symmetry matrices

iv. Change optional parameters if desired

b. Enter center of unit cell in symmetry matrix file

c. Run XPLOR

 

Detailed instructions

a. Edit fcalc.inp, a script file for XPLOR that will calculate structure factors

i. Set unit cell values to your chosen unit cell size (e.g. "a=600.0 b=600.0 c=600.0")

ii. Set resolution. For example, for infinity to 25.0 Å use "resolution INFINITY 25.0"

iii. Enter a filename for non-crystallographic symmetry matrices. Use ncs_center_icosahedral.mat for icosahedral symmetry or ncs_center_asymmetric.mat for an asymmetric object. (This file will be edited in step b.) If you need to apply another symmetry you will need to generate this file.

iv. Other parameters that may be changed

-temperature factor ("b=2000.0"), 2000 works well for icosahedral viruses at moderate resolutions

-"nreflections" should overestimate the number of reflections. Increase if necessary.

-The line "symmetry = (x, y, z)" refers to crystallographic symmetry only. Change if you wish to apply crystallographic symmetry.

-"grid = X" means program will use default grid size which is 1/3 of resolution. You could use a finer grid if you so wish, like "grid = 0.2"

-Scaling output. In fcalc.inp, the line "do amplitude (fcalc=0.001*fcalc)" scales the output structure factors by 0.001. You may wish to change this. Alternatively, the densities can be scaled after they are computed in step 4.

-An exclamation point (!) at the beginning of a line will cause the program to ignore the line.

b. Edit symmetry matrices file, the file chosen in step a.iii. On line 6, change translation values to 1/2,1/2,1/2 of your unit cell. The "skew" on line 2 means the translation will apply to all other matrices, if present.

c. Run XPLOR. Script file fcalc.inp is input. In UNIX, execute command "xplor < fcalc.inp > fcalc.out". Other necessary files are generate.psf and generate.pdb from step 2, the XPLOR parameter file parhcsdx.pro, and the symmetry matrices file. Output is fc.xpl and fcalc.out (log file, if above UNIX command is used).