Parameter File Outputs, Latest Version vs Version 7.07

Hi Kevin,

1) In the output parameter file, phase residuals have been replaced with a score to indicate the quality of fitting where a high number indicates good fit. What is the range of these scores?

I believe the range of the scores is 0-90, but it might be 0-100. A good score is usually in the 20-50 range, depending on the size of the particle, and resolution shells you are including in the refinement.

2) In the output parameter file, what do the numbers for OCC, -LogP and Sigma mean?

OCC is occupancy, and is used in classification (See Lyumkis et al, 2013)

-LogP is the negative of the log probability of data given the model (it is a kind of score) , and is used in the classification (See Lyumkis et al, 2013)

Sigma is an estimate of the variance of the noise.

3) Can I use a parameter file from the older version that doesn't have the changes listed above for refinement in the latest version? If not, then would I need to convert the file or it is not compatible at all?

No, you can convert it using the following awk one-liner, assuming you have a single class in a frealign v8.10 or earlier version parameter file.

grep -v C parfile1 |
awk '{printf "%7d%8.2f%8.2f%8.2f%10.2f%10.2f%8d%6d%9.1f%9.1f%8.2f%8.2f%10d%11.2f%8.2f%8.2f\n",FNR,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,100,5000,1.0,35,0}' > parfile2

HTH,

Axel