VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 11 2004 - 14:29:47 CST

Hi,
  Ah, there's only ONE occupancy value for all timesteps in a
trajectory, so enabling the update color/selection every frame
won't do you any good. If you want to color multiple timesteps
differently, you'll need to save these data values into the "User"
field instead of the occupancy field. I've attached a simple script
illustrating how to use the user field to color something that's
time varying.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 11, 2004 at 05:47:40PM +0100, Florian Barth wrote:
> Hello John,
>
> thanks for the help. Unfortunately, all the conformations still have the
> same color. I set the color scale and played with the "update selection
> every frame" and "update color every frame" switches without success.
> I have included a short part of the pdb file below. The numbers in the
> occupancy field represent the docked enery of a conformation.
>
> Regards
>
> Florian Barth
>
> John Stone wrote:
> >Hi,
> > The automatic normalization you asked about is controlled by the
> >color scale settings in the 'trajectory' tab of the graphical
> >representations window. If you set the "color scale data range"
> >manually, VMD will not use the normalized values and will instead use the
> >values you select as the min/max values between which a color ramp is
> >generated. Let us know if you need more help with this.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Wed, Mar 10, 2004 at 02:10:27PM +0100, Florian Barth wrote:
>
>
>
>
> MODEL 1
> ATOM 1 C5 CIH 459 59.049 35.405 44.505 10.51
> ATOM 2 H10 CIH 459 59.308 36.281 43.911 10.51
> ATOM 3 H11 CIH 459 58.111 35.029 44.099 10.51
> ATOM 4 C4 CIH 459 58.836 35.828 45.960 10.51
> ATOM 5 H8 CIH 459 59.628 36.514 46.254 10.51
> ATOM 6 H9 CIH 459 58.933 34.957 46.605 10.51
> ATOM 7 C3 CIH 459 57.479 36.489 46.204 10.51
> ATOM 8 H6 CIH 459 56.797 35.762 46.643 10.51
> ATOM 9 H7 CIH 459 57.042 36.780 45.250 10.51
> ATOM 10 C2 CIH 459 57.557 37.717 47.114 10.51
> ATOM 11 H4 CIH 459 57.286 38.604 46.545 10.51
> ATOM 12 H5 CIH 459 58.585 37.863 47.434 10.51
> ATOM 13 C1 CIH 459 56.656 37.610 48.343 10.51
> ATOM 14 H1 CIH 459 56.051 38.503 48.467 10.51
> ATOM 15 H2 CIH 459 55.982 36.762 48.262 10.51
> ATOM 16 H3 CIH 459 57.243 37.480 49.248 10.51
> ATOM 17 C6 CIH 459 60.135 34.341 44.337 10.51
> ATOM 18 H12 CIH 459 60.785 34.620 43.510 10.51
> ATOM 19 H13 CIH 459 60.762 34.324 45.225 10.51
> ATOM 20 C7 CIH 459 59.576 32.939 44.087 10.51
> ATOM 21 H14 CIH 459 58.508 33.013 43.887 10.51
> ATOM 22 H15 CIH 459 60.027 32.532 43.184 10.51
> ATOM 23 C8 CIH 459 59.811 31.977 45.253 10.51
> ATOM 24 H16 CIH 459 59.062 32.153 46.021 10.51
> ATOM 25 H17 CIH 459 60.770 32.196 45.712 10.51
> ATOM 26 C9 CIH 459 59.773 30.505 44.841 10.51
> ATOM 27 H18 CIH 459 59.138 29.922 45.502 10.51
> ATOM 28 H19 CIH 459 59.357 30.380 43.846 10.51
> ATOM 29 C10 CIH 459 61.153 29.849 44.842 10.51
> ATOM 30 O2 CIH 459 61.776 29.524 43.884 10.51
> ATOM 31 O1 CIH 459 61.612 29.670 46.080 10.51
> ATOM 32 H20 CIH 459 61.945 30.505 46.394 10.51
> ENDMDL
> MODEL 2
> ATOM 1 C5 CIH 459 39.053 55.570 51.434 8.89
> ATOM 2 H10 CIH 459 38.488 55.413 52.352 8.89
> ATOM 3 H11 CIH 459 38.814 54.731 50.782 8.89
> ATOM 4 C4 CIH 459 40.549 55.550 51.754 8.89
> ATOM 5 H8 CIH 459 40.707 55.935 52.760 8.89
> ATOM 6 H9 CIH 459 41.069 56.231 51.083 8.89
> ATOM 7 C3 CIH 459 41.172 54.159 51.642 8.89
> ATOM 8 H6 CIH 459 41.191 53.854 50.597 8.89
> ATOM 9 H7 CIH 459 40.540 53.438 52.159 8.89
> ATOM 10 C2 CIH 459 42.590 54.080 52.213 8.89
> ATOM 11 H4 CIH 459 42.545 54.151 53.298 8.89
> ATOM 12 H5 CIH 459 43.162 54.940 51.875 8.89
> ATOM 13 C1 CIH 459 43.324 52.800 51.820 8.89
> ATOM 14 H1 CIH 459 44.366 52.834 52.125 8.89
> ATOM 15 H2 CIH 459 42.871 51.929 52.286 8.89
> ATOM 16 H3 CIH 459 43.299 52.648 50.745 8.89
> ATOM 17 C6 CIH 459 38.593 56.871 50.774 8.89
> ATOM 18 H12 CIH 459 38.086 57.488 51.513 8.89
> ATOM 19 H13 CIH 459 39.463 57.438 50.450 8.89
> ATOM 20 C7 CIH 459 37.663 56.649 49.581 8.89
> ATOM 21 H14 CIH 459 37.451 57.609 49.112 8.89
> ATOM 22 H15 CIH 459 38.182 56.054 48.831 8.89
> ATOM 23 C8 CIH 459 36.348 55.964 49.956 8.89
> ATOM 24 H16 CIH 459 35.876 56.511 50.767 8.89
> ATOM 25 H17 CIH 459 36.558 54.972 50.344 8.89
> ATOM 26 C9 CIH 459 35.368 55.852 48.788 8.89
> ATOM 27 H18 CIH 459 34.352 55.678 49.134 8.89
> ATOM 28 H19 CIH 459 35.329 56.770 48.209 8.89
> ATOM 29 C10 CIH 459 35.718 54.720 47.822 8.89
> ATOM 30 O2 CIH 459 36.533 53.875 47.998 8.89
> ATOM 31 O1 CIH 459 34.985 54.777 46.711 8.89
> ATOM 32 H20 CIH 459 35.485 55.250 46.052 8.89
> ENDMDL
> MODEL 3
> ATOM 1 C5 CIH 459 49.903 43.540 49.715 6.82
> ATOM 2 H10 CIH 459 50.259 42.875 50.501 6.82
> ATOM 3 H11 CIH 459 48.815 43.523 49.772 6.82
> ATOM 4 C4 CIH 459 50.345 42.996 48.355 6.82
> ATOM 5 H8 CIH 459 50.410 43.817 47.644 6.82
> ATOM 6 H9 CIH 459 49.581 42.322 47.972 6.82
> ATOM 7 C3 CIH 459 51.685 42.262 48.404 6.82
> ATOM 8 H6 CIH 459 52.390 42.838 49.003 6.82
> ATOM 9 H7 CIH 459 52.107 42.214 47.401 6.82
> ATOM 10 C2 CIH 459 51.583 40.846 48.973 6.82
> ATOM 11 H4 CIH 459 51.923 40.133 48.225 6.82
> ATOM 12 H5 CIH 459 50.540 40.611 49.167 6.82
> ATOM 13 C1 CIH 459 52.390 40.656 50.256 6.82
> ATOM 14 H1 CIH 459 53.284 40.066 50.075 6.82
> ATOM 15 H2 CIH 459 52.702 41.612 50.668 6.82
> ATOM 16 H3 CIH 459 51.805 40.145 51.015 6.82
> ATOM 17 C6 CIH 459 50.402 44.960 49.990 6.82
> ATOM 18 H12 CIH 459 51.474 44.933 50.176 6.82
> ATOM 19 H13 CIH 459 50.262 45.569 49.099 6.82
> ATOM 20 C7 CIH 459 49.703 45.629 51.174 6.82
> ATOM 21 H14 CIH 459 49.766 46.711 51.059 6.82
> ATOM 22 H15 CIH 459 48.642 45.383 51.146 6.82
> ATOM 23 C8 CIH 459 50.285 45.226 52.529 6.82
> ATOM 24 H16 CIH 459 51.330 45.521 52.575 6.82
> ATOM 25 H17 CIH 459 50.275 44.144 52.617 6.82
> ATOM 26 C9 CIH 459 49.538 45.836 53.715 6.82
> ATOM 27 H18 CIH 459 48.521 46.111 53.448 6.82
> ATOM 28 H19 CIH 459 49.447 45.130 54.536 6.82
> ATOM 29 C10 CIH 459 50.217 47.089 54.268 6.82
> ATOM 30 O2 CIH 459 50.988 47.129 55.170 6.82
> ATOM 31 O1 CIH 459 49.842 48.183 53.607 6.82
> ATOM 32 H20 CIH 459 49.205 47.925 52.947 6.82
> ENDMDL
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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