Loading input files¶

fetch 2gb1: loads a pdb/cif file

set assembly, 1; fetch 6bb5, 6bb5_full loads a biological unit 1 for the 6bb5 as 6bb5_full

Selecting stuff¶

select resn hem selects by residue name

select resi 12+13+14 selects three residues by residue index

select bb, name C+N+CA+O selects protein backbone atoms by name, selection is stored under the name bb (as backbone)

select sidechains_A, chain A and (not bb) selects sidechains from chain A just by selecting anything that is not backbone

select segment, resi 155-167 selects three residues and names them segment

select !polymer selects all water molecules, bufefer, cofactors etc

See also selection algebra 2 page on PyMOL wiki

Hide & Show¶

show surface shows surface for the whole object

hide cartoon hides all cartoons

show sticks, segment show the object “segment” as sticks

set seq_view, on shows the sequence

to display a CA trace with sticks connecting:

```

set ribbon_trace,1 set ribbon_sampling,1 show ribbon

```

Extract, copy or remove¶

remove solvent: remove solvent (water molecules)

remove resn hoh: remove residues by name - in this case also removes water molecules

Working with electron density¶

fetch 3av2, type=2fofc download the 2fofc electron density map; Note, that the density will be loaded into an object named 3av2_2fofc

map_double 3av2_2fofc doubles the grid for electron density map tabulation

isomesh 3av2_mesh, 3av2_2fofc, 2.0 create a mesh object named 3av2_mesh for the whole cell, using the density map 3av2_2fofc; use sigma=2.0 when displaying

isomesh map, 3av2_2fofc, 2.0, 3av2 draws a mesh just for the 3av2 object

Miscellanea¶

reinit: clear and delete everything

get_symmetry object-name: prints unit cell parameters and space group name as e.g. “P212121”

References

1: https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies
2: https://pymolwiki.org/index.php/Selection_Algebra