Collection of pymol scripts written primarily for Giovanni Maglia's group members (website, university page)
Copy paste run https://raw.githubusercontent.com/mjtadema/public_pymol_scripts/master/loader.py into your own pymolrc file. This will make PyMOL load the scripts automatically at startup.
DESCRIPTION Split object into chains. By default chains are also colored.
ARGUMENTS object: object to split (default: top object) color: color by chain (default: 1)
EXAMPLE split_chains obj01 split_chains color=0
SEE ALSO merge_chains
DESCRIPTION Clip a selection through the ZY-plane of its principal axes
ARGUMENTS selection: selection string cut_range: slab thickness view_key: optionally store the resulting view as an F key
EXAMPLE carve carve obj1 carve obj1, 20 carve obj1, view_key=F1
DESCRIPTION Axes script (Based on https://pymolwiki.org/index.php/Axes) Show axes with nice cylinders and cones. By default it will move with the viewport and stay in the corner. Can be made to stay at 0,0,0 as well.
ARGUMENTS name: axes object name zero: keep axis object at zero (default: 0)
EXAMPLE axes axes new_axes axes center_axes, zero=1 axes zero=1
DESCRIPTION Calculate distances between all atoms in selection1 and selection2, then make a distance object for the smallest distance.
If you want to calculate the shortest distance for a very
large selection, consider installing anaconda (https://www.anaconda.com/).
Anaconda provides numpy which is needed for faster calculations.
ARGUMENTS selection1 : selection string for atoms in the first selection selection2 : selection string for atoms in the selection selection n : number of distances to calculate (default: 1) t : threshold of number of atoms if using non-numpy calculation (default: 500) unique : only one distance per residue (default: 0 (0=no, 1=yes))
EXAMPLE mindist chain A, chain D mindist chain A, chain D, n=10, unique=1
DESCRIPTION Do mutations on an entire selection at once. Use default rotamers (by default the lowest strain).
ARGUMENTS selection : selection string, all residues are mutated to the same resname resname : name of the residue to mutate to, can be one or three letter code
EXAMPLE mutate resi 10, ARG mutate resi -1, A mutate resi 12 and chain A, G
DESCRIPTION Print the fasta sequence of a selection
ARGUMENTS selection: selection string
EXAMPLE fasta chain A
DESCRIPTION Transform a selection such that its principle axes are aligned with the x, y, z axes
ARGUMENTS selection: a selection string
EXAMPLE princ_align obj01
DESCRIPTION Merge chains back into a common object
ARGUMENTS name: base name of the original object
EXAMPLE split_chains obj merge_chains obj
SEE ALSO split_chains