PyMOL advanced

Inne, nie mniej ciekawe.

Galeria do przećwiczenia (z przykładami) 📌

• http://pymolwiki.org/index.php/Gallery 📌
• http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol

Pocket finding

• To display the external surface of interior cavities and pockets, click on Setting → Surface → Cavities & Pockets Only.
• show surface
• By default, the cavity detection radius and cavity detection cutoff are set at 5 solvent radii and 3 solvent radii, respectively. Adjust these settings to reveal potentially important pockets and cavities of different sizes.
• set surface_color, orange
• set transparency, 0.2

http://www.biochemistry.ucla.edu/biochem/Faculty/Hubbell/protocols/Displaying%20cavities%20with%20PyMOL.pdf

Skrypty

run /home/fstefaniak/sources/color_by_mutation_pymol.py

Command line:

# labels
label i. 31 and n. P and 5E54, "5E54"
set label_position,(3,1,1)

# iteracje
models=cmd.get_names(); for model in models: print(model); cmd.select("selection","i. 31 and n. P and %s" % model); cmd.label("selection", "AAA")
# nie działa label

APBS

• ustawić ścieżki do programów, np:
• psize.py: /usr/share/pdb2pqr/src/psize.py
• pdb2pqr.py: /usr/share/pdb2pqr/pdb2pqr.py
• Selection to use: nazwa makromolekuły
• set grid
• run APBS