Tuesday, 5 February 2019

PDB in Office 365

Today I noticed that Word and the rest of Office 365 (i.e. Powerpoint included) can read .obj files (Wavefront files).
This means that I can export in PyMol (via the command "save whatever.obj") a .pse/.pdb to .obj file and open it in Word or Powerpoint or even Outlook. Quite fun and potentially useful little feature. Do note that colours are obviously lost, so it is a bit limiting. The loss of colour is due to PyMOL (Blender exported Wavefront files are textured). Also, only the cartoon of every residue is given, not only visible, and all sticks etc. are lost.

Tuesday, 15 January 2019

Phosphorylated PDB files

Sometime in human protein, a residue is phosphorylated, yet the model one gets from I-TASSER, Phyre etc. or the actual PDB structure lacks these. Here is how to add them easily and quickly with Rosetta.