Pymol

© pymol

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View and Themes

background color

bg_color grey30

Add something

Add Hydrogen bonds

Add Hydrogen bonds: PyMOL tutorial

Action → find → polar contacts → select from menu

© PyMOL tutorial

Remove something

cite: © Jan-Philip Gehrcke; 2011

# removing hydrogens
remove (hydro)
remove hydrogens
# removing water
remove resn hoh
# removing solvent
remove solvent

Strcture align

© Pymol

fetch 1oky 1t46, async=0
# 1) default with outlier rejection
align 1oky, 1t46
# 2) with alignment object, save to clustalw file
align 1oky, 1t46, object=alnobj
save alignment.aln, alnobj
# 3) all-atom RMSD (no outlier rejection) and without superposition
align 1oky, 1t46, cycles=0, transform=0

Partial structure align

Cite: Queen’s University

align 5cha and resi 1-100, 2xxl and resi 300-400
# or in short form:
align structure2 & i. 1-100, structure 1 & i. 300-400

# Furthermore, you may wish to restrict the alignment to just the backbone atoms, so you can say:

align structure2 and resi 1-100 and name n+ca+c+o, structure1 and resi 300-400 and name n+ca+c+o

# or in short form:

align structure2 & i. 1-100 & n. n+ca+c+o, structure1 & i. 300-400 & n. n+ca+c+o

Align chains

align 5cha and chain A+B+C, 2xxl and chain A

Atom

Atom color

## change the whole proteins color
color grey90, 2xxl
color grey80, 2xxl 5cha # 2 proteins

Select Atom

Select Properties

select aas, resn ASP+GLU in 2xxl

Create a variate ass which contain all ASP and GLU residues.

Enjoy~

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