Pymol Color By Data

:: pymol

This post expands on info from a few other blog posts.

  1. Your data should be in a tab-delimited text file, formatted like this:

    3	0.677985
4	0.794402
5	0.972709

  2. You may need to remove extra columns and/or headerscan cause problems. If you exported your file from excel, you may have to change your line break format. From a mac, you might see a bunch of ^M characters in your file. You can use a terminal to do one of these commands to fix the file:

    tr '\r' '\n' < macfile.txt > unixfile.txt
tr -d '\r' < windowsfile.txt > unixfile.txt
  3. Save this data file to a known location, let’s say /Users/username/Documents/datafile.txt. It might make things easier to avoid having spaces in file or folder names. It seems to be important to use the absolute filename, rather than using shortcuts like ~.
  4. Download data2bfactor.py from http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/.
  5. Download spectrumany.py from http://pymolwiki.org/index.php/Spectrumany.
  6. Save these scripts to a known location, let’s say ~/scripts/.
  7. Open pymol & load your protein structure.

  8. Run the scripts you downloaded using the PyMOL> commandline:

    PyMOL> run ~/scripts/data2bfactor.py
PyMOL> run ~/scripts/spectrumany.py

  9. Make a named selection for the set of residues you want to color:

    PyMOL> select MyChainA, 3TGN and chain A and not resn Zn

  10. You may want to set all the b-factor data for your selection to 0 or to some other number beforehand, because any residues not mentioned in your data file will retain their original crystallographic B-factor:

    PyMOL> alter MyChainA, b=0

  11. Now load your data onto your selection using the data2b_res function defined within data2bfactor.py:

    PyMOL> data2b_res MyChainA, /Users/username/Documents/datafile.txt

  12. Now color by B-factor. If you are lucky and the color gradient you want is already included in Pymol, you can use the function spectrum:

    PyMOL> spectrum b, rainbow, MyChainA, minimum=0.6, maximum=1
  13. You will need to play around with minimum and maximum to optimize the image according to your data.

  14. If you want a color gradient not already defined in Pymol, you will need to use the spectrumany command:

    PyMOL> spectrumany b, red gray80, MyChainA, minimum=0.6,maximum=1

  15. Now use the Display menu to make sure the Background is not set to be opaque, and ray trace the image:

    PyMOL> ray
  16. Save your image and your session!