Hi there,
I understand one can use the mouse to click the control panel to show disulphide bonds on the protein, but just out of curiosity, is there any command line that is able to do the same, which is to show the disulphide bonds on a certain object?
select SSbond, CYS/SG and bound_to CYS/SG
show sticks, SSbond
You can further refine the selection by specifying the object, chain, range of residues etc.
example:
#load antibody
fetch 1igt
color slate, chain B+D
color pink, chain A+C
color white, hetatm
#show hinge disulphides
select hingeSS, (/1igt/B/B/CYS/SG and bound_to /1igt/D/D/CYS/SG) or (/1igt/D/D/CYS/SG and bound_to /1igt/B/B/CYS/SG)
show sticks, hingeSS
color yellow, hingeSS
#since this shows only the bond between the sulfur atoms, you may want to expand the selection to the entire cystein residue
show sticks, br. hingeSS
color yellow, br. hingeSS
Similarely, you can selectively display the disulfide bonds between light and heavy chain and the various intradomain disulfide bonds
show sticks, byres elem S within 3 of elem S
This will show all bound sulfur atoms in the model, no matter what protein you are using.
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