Molscript-multicoloured beta-strands

Paul Davis Paul at pdchem.demon.co.uk
Mon Oct 11 06:38:40 EST 1999


Dear Steffen,

I'm sorry I did not explain in sufficient detail. Here's an
input file to illustrate what I do.

                           --ooOoo--


! MolScript v2.0 input file
! generated by MolAuto v1.0.1

! REM MODIFIED BY HAND TO COLOUR RESIDUES 33 AND 35

title "CRAMBIN"

plot

  read mol "1crn.pdb";

  transform atom * by centre position atom *;

  set segments 2;
  
 
  set colourparts on;
   
  set residuecolour residue 1 hsb 0.6667 1 1;
  set residuecolour residue 2 hsb 0.6667 1 1;
  set residuecolour residue 3 hsb 0.6667 1 1;
  set residuecolour residue 4 hsb 0.6667 1 1;
  strand from 1 to 4;

  set residuecolour residue 4 hsb 0.5714 1 1;
  set residuecolour residue 5 hsb 0.5714 1 1;
  set residuecolour residue 6 hsb 0.5714 1 1;
  set residuecolour residue 7 hsb 0.5714 1 1;  
  coil from 4 to 7;

  set residuecolour residue 7 hsb 0.4762 1 1;
  set residuecolour residue 8 hsb 0.4762 1 1;
  set residuecolour residue 9 hsb 0.4762 1 1;
  set residuecolour residue 10 hsb 0.4762 1 1;
  set residuecolour residue 11 hsb 0.4762 1 1;
  set residuecolour residue 12 hsb 0.4762 1 1;
  set residuecolour residue 13 hsb 0.4762 1 1;
  set residuecolour residue 14 hsb 0.4762 1 1;
  set residuecolour residue 15 hsb 0.4762 1 1;
  set residuecolour residue 16 hsb 0.4762 1 1;
  set residuecolour residue 17 hsb 0.4762 1 1;
  set residuecolour residue 18 hsb 0.4762 1 1;
  set residuecolour residue 19 hsb 0.4762 1 1;
  helix from 7 to 19;

  set residuecolour residue 19 hsb 0.381 1 1;
  set residuecolour residue 20 hsb 0.381 1 1;  
  set residuecolour residue 21 hsb 0.381 1 1;
  set residuecolour residue 22 hsb 0.381 1 1;
  set residuecolour residue 23 hsb 0.381 1 1;
  coil from 19 to 23;
  
  set residuecolour residue 23 hsb 0.2857 1 1;
  set residuecolour residue 24 hsb 0.2857 1 1;
  set residuecolour residue 25 hsb 0.2857 1 1;
  set residuecolour residue 26 hsb 0.2857 1 1;
  set residuecolour residue 27 hsb 0.2857 1 1;
  set residuecolour residue 28 hsb 0.2857 1 1;
  set residuecolour residue 29 hsb 0.2857 1 1;
  set residuecolour residue 30 hsb 0.2857 1 1;
  helix from 23 to 30;

  set residuecolour residue 30 hsb 0.1905 1 1;
  set residuecolour residue 31 hsb 0.1905 1 1;
  set residuecolour residue 32 hsb 0.1905 1 1;
  coil from 30 to 32;

!  set residuecolour residue 32 hsb 0.09524 1 1;
 set residuecolour residue 32 cyan;
  set residuecolour residue 33 hsb 0.09524 1 1;
  set residuecolour residue 34 hsb 0.09524 1 1;
!  set residuecolour residue 35 hsb 0.09524 1 1;
 set residuecolour residue 35 purple;  
  strand from 32 to 35;

  set residuecolour residue 35 hsb 0 1 1;
  set residuecolour residue 36 hsb 0 1 1;
  set residuecolour residue 37 hsb 0 1 1;
  set residuecolour residue 38 hsb 0 1 1;
  set residuecolour residue 39 hsb 0 1 1;
  set residuecolour residue 40 hsb 0 1 1;
  set residuecolour residue 41 hsb 0 1 1;
  set residuecolour residue 42 hsb 0 1 1;
  set residuecolour residue 43 hsb 0 1 1;
  set residuecolour residue 44 hsb 0 1 1;
  set residuecolour residue 45 hsb 0 1 1;
  set residuecolour residue 46 hsb 0 1 1;
  coil from 35 to 46;

end_plot

                           --ooOoo--

On 8 Oct, in article <7tkmha$j6n$1 at knot.queensu.ca>
     steffen at protein.biochem.queensu.ca "Steffen Graether" wrote:

> In article <939372879snz at pdchem.demon.co.uk> you wrote:
> > In your Molscript input file, you might try something like this:-
> 
> >   set colourparts on;
> >   set residuecolour residue 354 green;
> 
> That partly works. The problem with colourparts on is that the colour of 
> the strand extends into neighbouring coil regions, rather than starting 
> at the strand. If I make the coil region a little longer then the colour 
> of the coil extends into the helix. Either way, the structure looks bad 
> with these 'strange' transitions. I've tried mixing colourparts on and 
> off, but then the coils are no longer continuous.
> 
> Steffen
> 
> 
-Paul
-- 

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Paul Davis                                   paul at pdchem.demon.co.uk





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