Mark A. White wrote:
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>
> I have a couple of simple awk commands that will calculate both I/sI and
> Redundancy, by
> parsing the the scalepack output log.
> ### I/sigma by Shell
> awk '{ if ($11 > 1. && ($1>$2 || $2=="hkl")) printf"Sig: %7.2f%5.2f %8.1f
> \n",$1,$2,(0.5*($4-$3)+($5-$4)+2.5*($6-$5)+4.5*($7-$6)+7.5*($8-$7)+15*($9-$8)+25*$10)/($11+0.01)
>
> }' scalepack.log | tail -16
> #### Redundancy by Shell
> awk '{ if ($13 > $3 && ($1>$2 || $2=="hkl")) printf"Red: %7.2f%5.2f %8.1f
> \n",$1,$2,($4+2*$5+3*$6+4*$7+5.3*$8+7.3*$9+10*$10+14*$11+1337*$12)/($13+0.01)
> }'
> scalepack.log | tail -16
>
> PS. You will probably need to reassemble the above commands. Each one is a
> single command
> line, which can be placed at the end of your scalepack.com script. Note that
> I usually use
> 15 resolution shells, so that the output of each command is truncated to 16
> lines,
> otherwise you get a lot of junk, particularly from the latest versions of
> scalepack.
> Change the "tail" command to limit your output to the number of resolution
> shells plus 1.
>
>
> [email protected] wrote:
>
>>
>> I've written an awk/nawk script that will post-process a Scalepack log file
>> to produce
>> pseudo <I/SIGI> values as a function of resolution, as well as the (pseudo)
>> overall
>> value. It does this by massaging the "I/Sigma in resolution shells" table,
>> calculating a
>> pseudo <I/SIGI> weighted by the number of reflections in each individual
>> I/SIGI//resolution bin. (Some counting of number of reflections is also
>> corrected.) This
>> process is obviously an inaccurate, stopgap measure, but some would argue
>> that it is
>> better than nothing. Perhaps the next update of Scalepack will report more
>> complete
>> statistics, along the lines of Scala?
>> ~~~~~~~~~~~~~~~~~~~~~~~~
>> David Borhani, Ph.D.
>> Group Leader, Biochemistry
>> Vox: 508-849-2944
>> Fax: 508-755-8361
>> Email: [email protected]
>> Smail: Abbott Bioresearch Center, Inc.
>> 100 Research Drive
>> Worcester, MA 01605 U.S.A.
>> http://abbott.com/abbottbioresearch/
>> ~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> # awk/nawk file
>> # DWB 1Oct2003
>> #
>> # Extract <I/SigI> statistics as a function of resolution from a scalepack
>> log file.
>> #
>> # Usage:
>> #
>> # awk -f scalepack_Isig.nawk scalepack.log > scalepack.log.I_over_sigma
>> #
>> # Typical input data from a Scalepack log file:
>> #
>> # Shell I/Sigma in resolution shells:
>> # Lower Upper No. of reflections with I / Sigma less than
>> # limit limit 0 1 2 3 5 10 20 >20 total
>> # 50.00 3.21 26 51 73 101 163 335 707 8474 9181
>> # 3.21 2.55 110 214 315 410 609 1131 2521 6690 9211
>> # 2.55 2.23 206 383 608 815 1253 2197 4277 4879 9156
>> # 2.23 2.02 195 466 761 1051 1700 3119 5758 3388 9146
>> # 2.02 1.88 448 941 1464 1959 2863 4859 7434 1757 9191
>> # 1.88 1.77 664 1511 2344 3100 4420 6558 8520 575 9095
>> # 1.77 1.68 846 2131 3370 4420 5934 7891 9022 155 9177
>> # 1.68 1.61 1088 2852 4441 5629 7030 8529 9050 48 9098
>> # 1.61 1.54 1281 3455 5197 6204 7313 8206 8435 11 8446
>> # 1.54 1.49 685 1986 3076 3847 4671 5115 5162 2 5164
>> # All hkl 5549 13990 21649 27536 35956 47940 60886 25979 86865
>> #
>> #-----------------------------------------------------------
>> #
>> BEGIN {
>> # skip to correct start of table...
>> x = 0
>> y = 0
>> nrbins = 0
>> #
>> while (x != 1)
>> {
>> getline
>> if ($1 == "Shell" && $2 == "I/Sigma" && $4 == "resolution") {x = 1}
>> }
>> # Skip to " limit limit 0 1 2..." line, and load up I/Sigma bin
>> values...
>> getline ; getline
>> nibins = NF-3
>> for (i = 3; i <= NF-1; ++i)
>> {
>> # Force ">20" to be interpreted as "30.0"
>> if (substr($i,1,1) == ">") $i = substr($i,2,length($i)) * 1.5
>> # Force real value rather than text for all ibin values
>> ibin[i-2] = $i + 0.
>> }
>> }
>> #
>> # Process table data...
>> #
>> {
>> while (y != 1)
>> {
>> # Process regular lines of the table
>> if ($1 != "All")
>> {
>> # Increment resolution bin counter, store resolution limits for this line...
>> ++nrbins
>> rbin[1,nrbins] = $1
>> rbin[2,nrbins] = $2
>> # Store number of reflections in each I/SigI for this line...
>> for (i = 3; i <= nibins + 2; ++i) bin[i - 2,nrbins] = $i
>> getline
>> }
>> else
>> {
>> y = 1
>> }
>> }
>> }
>> #
>> END {
>> printf "Pseudo <I/sigI> Statistics from scalepack log file: %s\n\n",
>> FILENAME
>> printf " bin dmax dmin Nhkl <I/sigI>\n"
>> printf "----------------------------------------\n"
>> ntot = 0
>> isigtot = 0
>> # Loop over resolution bins...
>> for (j = 1; j <= nrbins; ++j)
>> {
>> n[j] = 0
>> isig[j] = 0
>> # Loop over I/SigI bins at given resolution...
>> for (i = 1; i <= nibins; ++i)
>> {
>> # Total number of reflections, calculate pseudo I/SigI...
>> n[j] = n[j] + bin[i,j]
>> isig[j] = isig[j] + bin[i,j] * ibin[i]
>> isigtot = isigtot + bin[i,j] * ibin[i]
>> }
>> # Overall statistics...
>> isig[j] = isig[j] / n[j]
>> ntot = ntot + n[j]
>> printf " %3i %6.2f %6.2f %8i %8.2f\n", j, rbin[1,j], rbin[2,j], n[j],
>> isig[j]
>> }
>> isigtot = isigtot / ntot
>> printf "----------------------------------------\n"
>> printf "OVERALL %6.2f %6.2f %8i %8.2f\n", rbin[1,1], rbin[2,nrbins], ntot,
>> isigtot
>> }
>> # END of awk/nawk file
>
>
