Side chains in molscript

Shoba Ranganathan shoba at angis.org.au
Mon Mar 29 20:43:15 EST 1999


Dear Steffen,

> I have a molscript ribbon diagram to which I've added some side chains
> using the ball-and-stick command. Unfortunately, the CA is not located on
> the ribbon because of coil smoothing. I really don't like these
> "disembodied" atoms, does anyone know of any tricks to make them connect
> back to the main chain?

In Molscript v.2.0 onwards, you can fix the Ca position as follows:

a. in coil regions, use turn instead. If adding side chain for residue
23, try:

coil from .. to 22;
turn from 22 to 24;
coil from 24 to ..;

Minimum for a turn is 2 residues but I get better results with 3.
The turn cammand is especially useful for showing disulfide bridges.

b. in strands, switch smoothing off with:
set smoothsteps 1;
strand from 20 to 24;
set smoothsteps 2; # default value

c. in helices, it is difficult to fix Ca's:  options are
1. choose a view where the Ca is not hanging in the air
2. increase the thickness of the helix with:
   set helixthickness 0.5; # default value is 0.3
3. try to adjust the Ca xyz coordinates ever so slightly (+/- 0.01) in the PDB
file
   to visually improve cartoon: this is tedious but possible for a few
residues.  

d. in cylinders, increase cylinder radius to establish connection with Ca:
set cylinderradius 2.4; # default 2.3

Shoba
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