There is some documentation at http://instinct.v24.uthscsa.edu/~hincklab/html/soft_utils/plotpseq.shtml
Example file1:
#DATA
BASE_NAME /instinct2/ahinck/af19/hncacb_fb.af19/1/data/testtp
X_OFFSET 0.000000
Y_OFFSET 0.000000
Z_OFFSET 0.000000
Z_PHASE_PAR 0
Y_LINE_WIDTH 0.06
Z_LINE_WIDTH 0.6
Y_WIDTH_P 0.25
Z_WIDTH_P 0.80
DISPLAY_FILTER 0
#DATA
#COMMANDS
;read_command_file strip_na.com
read_command_file strip.com
#COMMANDS
Sample file 2 (called strip.com and referred within file 1)
#COMMANDS
open hncacb.DAT 1
get_strip 1 7.885 128.06
get_strip 2 8.002 127.29
get_strip 3 8.372 127.43
get_strip 4 9.803 127.04
get_strip 5 8.550 126.90
get_strip 6 8.970 126.76
get_strip 7 9.194 126.55
get_strip 8 8.178 126.31
get_strip 9 8.694 126.23
get_strip 10 9.329 125.89
get_strip 11 8.168 125.35
get_strip 12 8.572 124.42
get_strip 13 7.837 124.34
get_strip 14 9.021 124.15
get_strip 15 8.959 123.77
get_strip 16 8.284 123.89
get_strip 17 8.399 123.66
get_strip 18 8.472 123.61
get_strip 19 8.586 123.30
get_strip 20 8.233 123.36
blank_strip
blank_strip
get_strip 23 8.105 122.36
blank_strip
get_strip 24 8.710 122.54
get_strip 25 9.399 122.12
get_strip 26 9.225 121.91
get_strip 27 7.201 122.07
get_strip 28 8.156 121.91
blank_strip
get_strip 30 8.212 121.50
get_strip 31 8.162 121.51
get_strip 31 9.319 121.20
get_strip 32 8.070 121.30
get_strip 33 7.994 121.06
get_strip 34 7.122 120.87
get_strip 35 8.377 120.69
get_strip 36 8.174 120.94
get_strip 37 7.977 120.80
get_strip 38 8.175 120.92
get_strip 39 8.867 120.61
get_strip 40 8.630 120.59
get_strip 41 7.293 120.33
get_strip 42 7.349 120.27
get_strip 43 8.111 120.58
get_strip 44 7.288 103.41
get_strip 45 8.216 107.71
get_strip 46 8.191 107.84
get_strip 47 7.803 109.20
get_strip 48 6.909 110.76
get_strip 49 6.989 111.08
get_strip 50 8.509 111.19
get_strip 51 8.256 112.29
get_strip 52 7.855 112.74
get_strip 53 7.312 113.46
get_strip 54 7.441 113.42
get_strip 55 8.207 113.72
get_strip 56 8.609 113.69
get_strip 57 8.344 114.02
blank_strip
get_strip 59 7.053 114.01
blank_strip
blank_strip
get_strip 62 8.454 114.28
get_strip 63 7.566 115.37
get_strip 64 7.349 116.11
get_strip 65 8.235 116.44
get_strip 66 7.384 116.89
get_strip 67 8.454 117.36
blank_strip
blank_strip
get_strip 70 8.543 117.70
get_strip 71 9.073 117.84
get_strip 72 9.159 117.82
blank_strip
get_strip 74 7.736 118.51
get_strip 75 7.996 118.41
get_strip 76 7.662 118.72
get_strip 77 6.708 118.80
get_strip 78 6.566 119.07
get_strip 78 8.430 118.74
get_strip 79 7.787 119.30
get_strip 80 7.836 119.07
get_strip 81 7.971 119.26
get_strip 82 8.068 119.24
get_strip 83 7.642 119.40
get_strip 84 8.097 119.40
get_strip 85 7.950 119.80
get_strip 86 7.550 119.83
get_strip 87 7.723 119.88
get_strip 88 8.489 119.99
get_strip 89 8.095 120.02
get_strip 90 8.319 120.37
get_strip 91 8.163 120.31
get_strip 92 8.027 120.29
get_strip 93 7.714 120.32
get_strip 94 8.091 120.33
get_strip 98 8.273 108.55
get_strip 99 7.236 114.44
get_strip 100 8.290 115.03
close
Issues:
The instructions say that the dimension to be extracted (C) must lie
along x. So starting from my
HCN dataset, I need to do a transpose. So I'll need a script
that's just xyz2pipe -x followed by pipe2xyz -y. I'll name the new
files testchn%03.dat.
Then there is the base name, which is the input without the number and the .DAT. Note: this program requires the extension to be .DAT in caps.
Y_WIDTH_P would then be peak width in ppm for H
Z_WIDTH_P would then be peak width in ppm for N
0.06 for H and 0.6 for N seem tight. They are more like .12 and 1.2; Are these half widths? Or are they set smaller than the peaks on purpose?
Y_LINE_WIDTH and Z_LINE_WIDTH are described as lorenzian linewidth in units of ppm for weighting data vectors along the dimension. I have no idea how to get these numbers, what they mean, or what weighting the algorithm is called upon to do. The example has 0.25 and 0.8, which are disproportionate to the actual widths and don't make any senze as a peak at half height??? See what's in some real data scripts. Andy basically uses these numbers.
Strip.com
The first entry is the name of the output file, which is a single file
The numbers aren't used; instead the data is displayed where the coordinate
number is strip
number in consecutive order. the Blank strip enties will also
be counted. (It's set up so that
you could enter the coordinates in the order of the amino acid sequence,
leaving out residues
that aren't in the dataset.
The only things that will likely be meaningfull in the strips are the
spots centered on the interger coordinate. A 2D Lorenzian peak is
forced. Other spots off the axis show up, but will be deformed.
The intention is that they would be centered up in another strip.