Step 3: Compute structure factors with CCP4

 

Overview

a. Edit sfall.sh command file.

i. Change filenames for input and output

ii. Set resolution maximum

iii. Set the temperature/B factor.

b. Run sfall.sh to compute structure factors

c. Check output log file for errors

Detailed instructions

a. Edit sfall.sh file, a command file that computes structure factors using CCP4.

i. Change the xyzin to refer to your sfall file in your area, and place the output file in the same directory. Change the name of the .log file.

ii. On the RESO line, change the value to the highest resolution (in Angstroms) structure factors desired. By choosing the highest resolution, only one run of sfall is required to produce the desired images (sfall is, by far, the slowest step in this procedure).

iii. Replace the number on the BRESETMIN line with the B factor (temperature factor) desired for the structure factor calculation.

b. Run the sfall.sh command file on your machine. You will probably want to run it in batch mode. Check with your system manager or a competent colleague for help in submitting a batch job on your system. For the icosahedral viruses we have tried, the jobs have taken a few hours to complete. It is by far the slowest step in the process. If you have problems running sfall, or wish to change parameters not discussed here, the documentation for the CCP4 programs is at http://www.dl.ac.uk/CCP/CCP4/dist/html/INDEX.html.

c. Once the sfall job has completed, view the log file to make sure everything ran okay. If it didn’t, check your sfall.sh file and make sure all the parameters are correct. Check your quota again and make sure you didn’t run out of disk space. Make sure you followed all previous steps.