Titration Data Analysis in nmrPipe: Difference between revisions
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1. Type “csh” in your terminal to get a c-shell | 1. Type “csh” in your terminal to get a c-shell | ||
2. In a directory that contains the data folders create an “in.list” file which lists your data directories (vertically): | 2. In a directory that contains the data folders create an “in.list” file which lists your data directories (vertically): | ||
000/5, 010/5, 020/5, etc… | |||
3. Run autoProc.com | 3. Run autoProc.com | ||
./autoProc.com | |||
4. Use ft.com to make corrections | 4. Use ft.com to make corrections | ||
5. Run setC.com | 5. Run setC.com | ||
Edit - fileCount - zT | |||
- zN - zSW | - zN - zSW | ||
dirList ligandCList proteinCList | dirList ligandCList proteinCList | ||
There is an nmrPipe titration tutorial that can be referenced if you need more help. | |||
6. Open as a data series. | 6. Open as a data series. | ||
nmrDraw ft/*.dat | |||
7. Peak detection, edit peak tables names. | 7. Peak detection, edit peak tables names. | ||
tab/test%03d.tab, click “Detect”, click “Save” | |||
8. Run view2D | 8. Run view2D | ||
view2D.tcl $* -export titrView –hi 2.2e+5 –in ft/*.dat –tab tab/*.tab | |||
Click “Start”, edit contours, click “Export Region”, edit peaks, click “Save” | |||
9. Run modelTitr | 9. Run modelTitr | ||
modelTitr.tcl –axis XY –sigma 0.002 –cy 0.25 | |||
cy is the ratio of direct to indirect dimension SW | |||
10. Run showTitr | 10. Run showTitr | ||
showTitr.tcl –in titrView.tab –var X_PPM Y_PPM –c 1.0 0.25 | |||
11. | 11. Use gnuFix.py to edit gnu scripts if necessary | ||
Revision as of 21:19, 14 March 2017
Titration Data Analysis in nmrPipe
1. Type “csh” in your terminal to get a c-shell
2. In a directory that contains the data folders create an “in.list” file which lists your data directories (vertically):
000/5, 010/5, 020/5, etc…
3. Run autoProc.com
./autoProc.com
4. Use ft.com to make corrections
5. Run setC.com
Edit - fileCount - zT
- zN - zSW
dirList ligandCList proteinCList
There is an nmrPipe titration tutorial that can be referenced if you need more help.
6. Open as a data series.
nmrDraw ft/*.dat
7. Peak detection, edit peak tables names.
tab/test%03d.tab, click “Detect”, click “Save”
8. Run view2D
view2D.tcl $* -export titrView –hi 2.2e+5 –in ft/*.dat –tab tab/*.tab
Click “Start”, edit contours, click “Export Region”, edit peaks, click “Save”
9. Run modelTitr
modelTitr.tcl –axis XY –sigma 0.002 –cy 0.25
cy is the ratio of direct to indirect dimension SW
10. Run showTitr
showTitr.tcl –in titrView.tab –var X_PPM Y_PPM –c 1.0 0.25
11. Use gnuFix.py to edit gnu scripts if necessary