pymol.txt

# Using the mouse
https://pymol.org/dokuwiki/doku.php?id=mouse:two_button
zoom: right click + drag

# Basics
hide all
show cartoon, vhh72
select T103,  chain A and resi 99
select delta_rbm, delta_rbd and pepseq NLDSKVGG  // select by sequence:w
label select, "name"
hide label // hide all labels
hide everything, hetatm // hide molecules

# General
set seq_view, on // show sequence (1 == on, 0 == off for hide)
bg_color white
remove solvent  // removes hydrogens and water molecules (HOH)
remove chain A  // removes the atoms (sequence) of chain A
delete sele // delects and object, .e.g. selection
reinitialize  // delete objects and reinitialize session
zoom 'visible'
origin vhh72 // sets vhh72 as the center of rotation
print(cmd.get_names('selections')) // show all selections
print(cmd.get_names('objects')) // show all object names selections

# Saving PDBs / Fasta
save seq.fasta, 6waq and chain A // save sequence of chain A  to fasta file
save seq.pdb, 6waq and chain A // save structure of chain A  to fasta file

# Files
pwd  // current directory
ls
cd

# Coloring
color atomic, not elem C  // color by element except C
spectrum b, red_yellow_green_cyan_blue,  vhh, minimum=50, maximum=90  // color by PDB properties, e.g. pLDDT

# Nice colors
firebrick
slate
deepteal
forest
smuge

# Settings
get label_size // return default setting
set label_size, 16
set label_font_id, 7 // bold style

# Python scripting
python  // start interpreter
python end // end interpreter
run script.py

# Special groups
NME:  N-methyl-amin; capping group
AME: Ammonium;  capping groups
NAG: Glucopyranose; glucose like