Difference between revisions of "Tutorial for Relaxation dispersion analysis cpmg fixed time recorded on varian as fid interleaved"

From relax wiki
Jump to navigation Jump to search
Line 14: Line 14:
 
You want to make a working dir, with different folders
 
You want to make a working dir, with different folders
  
<source lange="text">
+
<source lang="text">
 
peak_lists
 
peak_lists
 
spectrometer_data
 
spectrometer_data
Line 30: Line 30:
  
 
= Get the process helper scripts =
 
= Get the process helper scripts =
<source lange="bash">
+
<source lang="bash">
 
cd scripts
 
cd scripts
 
# Change shell
 
# Change shell
Line 51: Line 51:
 
= Extract interleaved spectra, process to NMRPipe and do spectral processing =
 
= Extract interleaved spectra, process to NMRPipe and do spectral processing =
 
== Extract interleaved and change format to NMRPipe ==
 
== Extract interleaved and change format to NMRPipe ==
<source lange="bash">
+
<source lang="bash">
 
# Copy data
 
# Copy data
 
cp -r spectrometer_data spectrometer_data_processed
 
cp -r spectrometer_data spectrometer_data_processed
Line 66: Line 66:
  
 
### Now it is time to convert all the fid from varian format.
 
### Now it is time to convert all the fid from varian format.
<source lange="bash">
+
<source lang="bash">
 
CPMG_2_convert_and_process.sh
 
CPMG_2_convert_and_process.sh
 
</source>
 
</source>
Line 85: Line 85:
 
As suggested in the [[Manual | relax manaul]], section '''5.2.2 Spectral processing''', the spectral processing script could look like:  
 
As suggested in the [[Manual | relax manaul]], section '''5.2.2 Spectral processing''', the spectral processing script could look like:  
 
File: '''nmrproc.com'''
 
File: '''nmrproc.com'''
<source lange="bash">
+
<source lang="bash">
 
#!/bin/csh
 
#!/bin/csh
  

Revision as of 08:04, 27 August 2013

Intro

This tutorial is based on the analysis of NMR data from the paper:

The inverted chevron plot measured by NMR relaxation reveals a native-like unfolding intermediate in acyl-CoA binding protein.
Kaare Teilum, Flemming M Poulsen, Mikael Akke.
Proceedings of the National Academy of Sciences of the United States of America (2006).
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458987

The data is recorded as FID interleaved

Preparation

You want to make a working dir, with different folders

peak_lists
spectrometer_data
scripts

You can create the folders by

mkdir peak_lists spectrometer_data scripts

In the folder spectrometer_data should be the files: fid and procpar as the output from recording fid interleaved on Varian.
In the folder peak_lists should contain SPARKY list in SPARKY list format. In the folder scripts we put scripts which help us processing the files.

Get the process helper scripts

cd scripts
# Change shell
tcsh
# Set array of scripts to download
set SCRIPTS="CPMG_1_sort_pseudo3D_initialize_files.sh CPMG_2_convert_and_process.sh CPMG_3_fft_all.sh convert_all.com fft_all.com sparky_add.sh stPeakList.pl NMRPipe_to_Sparky.sh"

# Download scripts
foreach SCRIPT ( ${SCRIPTS} )
curl https://raw.github.com/nmr-relax/relax_scripts/master/shell_scripts/$SCRIPT -o $SCRIPT
end

# Make them executable
chmod +x *.sh *.com *.pl

# Go back to previous directory
cd ..

Extract interleaved spectra, process to NMRPipe and do spectral processing

Extract interleaved and change format to NMRPipe

# Copy data
cp -r spectrometer_data spectrometer_data_processed

# sort_pseudo3D and initialize files
cd spectrometer_data_processed
CPMG_1_sort_pseudo3D_initialize_files.sh

Now we make a file to convert from binary format of Varian to NMRPipe.

  1. Now click, 'read parameters', check 'Rance-Kay'
  2. Remember to set Y-'Observe Freq MHz' to N15
  3. Click 'Save script' to make 'fid.com' file, and 'Quit', and run the next CPMG script
      1. Now it is time to convert all the fid from varian format.
CPMG_2_convert_and_process.sh

Spectral processing

  1. Now we need to spectral process the spectra.
  2. Process one of the files normally and the next script will copy the processing script to the other folder.
  3. [m]->Right-Click Process 2D->Basic 2D
  4. Save->Execute->Done; then; RClick File->Select File->test.ft2->Read/draw->Done
  5. If your spectra look reversed (i.e. if your peaks do not seem to match your reference spectrum) it might be solved by changing to
  6. [m] '| nmrPipe -fn FT -neg \' to the script to the third lowest line.
  7. Save->Execute->Done. Then push [r] to refresh.
  8. Press [h], and find P0 and P1, and push [m], change parameters and update script
  9. The changes to '| nmrPipe -fn PS xxx \' should be the FIRST line (The proton dimension) with PS
  10. save/execute, push [r] (read) and the [e] (erase settings) to see result in NMRdraw
  11. And then run the next CPMG script

As suggested in the relax manaul, section 5.2.2 Spectral processing, the spectral processing script could look like: File: nmrproc.com

#!/bin/csh

nmrPipe -in test.fid \
| nmrPipe  -fn SOL                                    \
| nmrPipe  -fn GM  -g1 5 -g2 10 -c 0.5                \
| nmrPipe  -fn ZF -auto -size 8000                    \
| nmrPipe  -fn FT -auto                               \
| nmrPipe  -fn PS -p0 214.00 -p1 -21.00 -di -verb     \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5    \
| nmrPipe  -fn ZF -auto -size 8000                    \
| nmrPipe  -fn FT -neg                                \
| nmrPipe  -fn PS -p0 0.00 -p1 0.00 -di -verb         \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn POLY -auto                             \
| nmrPipe  -fn EXT -left -sw                          \
   -ov -out test.ft2

See also