Molscript help needed desperately!

Kevin Gardner gardner at
Thu Aug 4 16:05:39 EST 1994

dirk (dirk at wrote:
: I'm tring to use the MOLSCRIPT program to plot out a helix from a
: structure and I would like to have the backbone of the helix as a coil
: and show !!only!! the side-chains as ball-and-stick models. 
: Unfortunately, I have only the manual (or should I say pamphlet) and no
: examples.  I've figured out how to draw the coil portion of the 
: diagram, but I can't seem to puzzle out
: MS's bizarre selection critieria for the ball-and-stick portion.  My
: scripts either won't run or draw ball-and-sticks of the entire main-
: and side-chains.  Can anyone out there give me some advice?  Thanks!
: -Dirk

Hi Dirk --- how's Duke?

You've got a couple of issues here (BTW, all examples are with
Molscript v1.4):

1).  Sidechain ball-and-stick:

You could do:

	ball-and-stick not backbone;

but that will omit the CA atoms, giving you disembodied sidechains
floating off of the mainchain.  Ghoulish and cool, but not the desired
effect.  Use this instead to get the CAs back online:

	ball-and-stick require atom * and not either atom N, atom C
		or atom O;

If you only want to run this over a range:

	ball-and-stick require atom *, not either atom N, atom C
		or atom O and in from 10 to 20;

If you've got some non-protein in your structure, switch to:

	ball-and-stick require atom *, in amino-acids and not either
		atom N, atom C or atom O;

I think you get the general drift here ---

2).  Helix representation:

You mentioned that you'd like to use a "coil" representation of the
helix section.  I'd avoid that; coil uses averaged CA positions except
for the first and last residue in the coil range.  Once again, you'll
get the cool disembodied sidechain effect.  Stick with "helix" 

Good luck!

Kevin Gardner				 
Yale University            Dept. of Molecular Biophysics and Biochemistry
Internet: gardner at               Bitnet: gardner at yalemed

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