Reduce Pymol Session (.Pse) File Size
Entering edit mode
11.0 years ago
Reyhaneh ▴ 530


I am using pymol to display a protein complex with 3 chains:

  • Two chains in cartoon mode (one with 800 residues and the other one with 300 residues).
  • The third chain in surface representation (300 residues).

I have also highlighted some specific residues in the display.

The problem is that I have saved it as a pymol session (.pse) file and the size of the file is around 3 M.

Do you know how to reduce the file size? I have tried removing some atoms but I will loose the cartoon (secondary structure) representations.

Thanks inadvance for the help.

P.S. If you are wondering why i need to reduce the size is because i want to use JSMOL to be able to show this model on mobile phones and since 3M is large it takes a while to load the figure. I would like to make it faster.

pymol protein • 4.5k views
Entering edit mode
11.0 years ago
Pappu ★ 2.1k

Zip, XZ, bz2 or 7z works quite well in reducing pse file size. Alternatively you can have a pml script to load with pdbs to show it in the way you want.

Entering edit mode
11.0 years ago

I don't get the point of needing a pymol session to display a complex.

Just use Jmol functionnalities to import the pdbs and compute/display what you want. You will get full control and reduce the size of the files to the size of your pdbs. If you enable mod_deflate/gzip of text files on your server you will gain in size too.


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