Notes on plotting 2DSA Grids

  • When an analysis request is created, a solutesTIMESTAMP.dat file is created, which contains the solutes
  • us_cmdline_t has an option to extract this info and create png images of gnuplots
    • requires gnuplot in path
    • example:
      $ us_cmdline_t plot_solutes solutes110108141013-0.dat solutes110108141013-0.txt
      base name ./solutes110108141013-0
      creating file: ./solutes110108141013-0-gnuplot.txt
      creating file: ./solutes110108141013-0-sall.txt
      creating file: ./solutes110108141013-0-s1.txt
      creating file: ./solutes110108141013-0-s2.txt
      creating file: ./solutes110108141013-0-s3.txt
      creating file: ./solutes110108141013-0-s4.txt
      $ ls -1st solutes*{txt,png}
      12 solutes110108141013-0-sallr.png
       4 solutes110108141013-0-sall.png
       4 solutes110108141013-0-s4.png
       4 solutes110108141013-0-s3.png
       4 solutes110108141013-0-s2.png
       4 solutes110108141013-0-s1.png
       4 solutes110108141013-0-gnuplot.txt
       4 solutes110108141013-0-s4.txt
       4 solutes110108141013-0-sall.txt
       4 solutes110108141013-0.txt
       4 solutes110108141013-0-s2.txt
       4 solutes110108141013-0-s3.txt
       4 solutes110108141013-0-s1.txt
  • Understanding the files created:
text file associated png contains
-sallr.png the png of all the gridpoints in a "replot" mode (i.e. each grid movement should be in a different color)
this seems only to contain the 1st set and appears be a bug with gnuplot when output is set to png
if you do the same commands (see -gnuplot.txt) in X11 output, it works fine
-sall.txt -sall.png the txt and png of all the gridpoints in a single plot
-s1.txt, -s2.txt, etc -s1.png, -s2.png, etc these contain the individual grids, there will be one for the original grid and one for each grid movement
-gnuplot.txt *.png these are the gnuplot commands.

us_gridcontrol_t new option

  • $ us_gridcontrol_t full-path/gcfile.gc none none plot
    • this will create the experiment & solute file and run us_cmdline_t on the files.
    • this could be called from the php
      1. setup a temporary directory
      2. copy the needed experiment files (e.g. what is staged before job submission in the php)
      3. run us_gridcontrol_t with the plot option
      4. retrieve appropriate png file "*-all.png" (for display in the browser)
      5. remove empty temporary directory
      6. even though the php submission info may not be completed, it should be possible to create an initial version of the .gc file to run this

Example mw 2dsa grid

mw range: 100 to 110 kD, resolution 5 ff0 range: 1 to 4, resolution 4

Here are the solutes for the base(unmoved) grid:

sedimentation coefficient frictional ratio molecular weight
8.27495e-131 100kD
4.13747e-132 100kD
2.75832e-133 100kD
2.06874e-134 100kD
8.4123e-131 102.5kD
4.20615e-132 102.5kD
2.8041e-133 102.5kD
2.10307e-134 102.5kD
8.54853e-131 105kD
4.27427e-132 105kD
2.84951e-133 105kD
2.13713e-134 105kD
8.68369e-131 107.5kD
4.34184e-132 107.5kD
2.89456e-133 107.5kD
2.17092e-134 107.5kD
8.8178e-131 110kD
4.4089e-132 110kD
2.93927e-133 110kD
2.20445e-134 110kD

Here's the picture:

  • Taking the ff0 2 group, the mw of the smallest s value has a mw of 100kD, the largest 110kD.
  • This was validated with UltraScan->Simulation->Predict f and axial ratios for 4 basic shapes.
    • There isn't a direct option for s & k to mw
    • I put the mw & s values for the smallest & largest s and the result was the correct f/f0
    • Here is the view from UltraScan->Simulation->Predict f and axial ratios for 4 basic shapes for the ff0 = 2 low & high mw components
      • us view of 100kD ff0=2 gridpoint
      • us view of 110kD ff0=2 gridpoint
Last modified 9 years ago Last modified on Jan 9, 2011 3:59:04 AM

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