VMD-L Mailing List

From: Matthew Geballe (mgeball_at_emory.edu)
Date: Wed Dec 08 2004 - 13:57:09 CST

Thanks for the swift replies...

On Dec 8, 2004, at 1:22 PM, Justin Gullingsrud wrote:
> That's right - Tube will work with just CA atoms, as will Trace, but
> the "anisotropic" reps like Ribbons need the whole protein backbone.
> However, CA atoms are apparently not enough to identify residues as
> protein residues.
>
> If you want to show all the sidechains, in addition to a tube for the
> entire chain, you could probably create two reps, one for "all" drawn
> as Tube, and a second for "same residue as sidechain" drawn as
> Licorice.

That is exactly what I would like to do, however the "all" drawn with
tube doesn't display the tube for all the CA atoms, only the ones that
have sidechains, or are a member of the "protein" selection. For this
same reason using the "alpha" selection also doesn't work. The "alpha"
selection is only CA atoms from the "protein" selection.

I've attached some small pdb structures that illustrate my problem.
They are very small and I hope they don't cause problems for anyone.

The first structure is only the CAs. If you select tube for this it
displays a tube for all the CA atoms. Note that if you change the
selection to protein the tube disappears. The tube representation is
displayed for all CA atoms even though they are not part of the
"protein" selection.

The second structure has the entire amino acid for 4 through 6.
Selecting tube here only displays the tube representation for residues
4 through 6. I can't figure out a way to display the tube for all the
CA atoms short of writing a custom script to display connections, and
I'm sure it wouldn't be as pretty as the tube representation.

Thanks again for the quick responses.
-Matt

HEADER Only CA atoms
MODEL 1
ATOM 2 CA LYS 1 24.121 0.549 22.271 1.00 32.05
ATOM 11 CA GLU 2 24.858 4.145 23.207 1.00 27.38
ATOM 20 CA THR 3 25.475 4.513 26.954 1.00 23.26
ATOM 27 CA ALA 4 23.646 7.264 28.928 1.00 19.56
ATOM 32 CA ALA 5 26.973 9.001 29.411 1.00 18.17
ATOM 37 CA ALA 6 27.667 8.723 25.675 1.00 17.62
ATOM 42 CA LYS 7 24.214 10.046 24.882 1.00 15.77
ATOM 51 CA PHE 8 24.684 13.122 27.093 1.00 11.39
ATOM 62 CA GLU 9 27.881 14.091 25.359 1.00 12.32
ATOM 71 CA ARG 10 26.217 13.615 22.008 1.00 12.35
30.373 21.916 1.00 29.66
TER
ENDMDL

HEADER All CA atoms and residues 4 to 6
MODEL 1
ATOM 2 CA LYS 1 24.121 0.549 22.271 1.00 32.05
ATOM 11 CA GLU 2 24.858 4.145 23.207 1.00 27.38
ATOM 20 CA THR 3 25.475 4.513 26.954 1.00 23.26
ATOM 26 N ALA 4 24.316 6.023 28.470 1.00 20.81
ATOM 27 CA ALA 4 23.646 7.264 28.928 1.00 19.56
ATOM 28 C ALA 4 24.622 8.442 28.958 1.00 18.79
ATOM 29 O ALA 4 24.267 9.606 28.686 1.00 17.61
ATOM 30 CB ALA 4 23.015 7.064 30.281 1.00 19.62
ATOM 31 N ALA 5 25.824 8.089 29.315 1.00 18.22
ATOM 32 CA ALA 5 26.973 9.001 29.411 1.00 18.17
ATOM 33 C ALA 5 27.301 9.459 27.996 1.00 18.37
ATOM 34 O ALA 5 27.487 10.671 27.734 1.00 18.89
ATOM 35 CB ALA 5 28.136 8.252 30.019 1.00 17.83
ATOM 36 N ALA 6 27.347 8.474 27.100 1.00 17.91
ATOM 37 CA ALA 6 27.667 8.723 25.675 1.00 17.62
ATOM 38 C ALA 6 26.563 9.530 25.053 1.00 17.34
ATOM 39 O ALA 6 26.910 10.405 24.191 1.00 18.24
ATOM 40 CB ALA 6 28.009 7.493 24.904 1.00 17.09
ATOM 42 CA LYS 7 24.214 10.046 24.882 1.00 15.77
ATOM 51 CA PHE 8 24.684 13.122 27.093 1.00 11.39
ATOM 62 CA GLU 9 27.881 14.091 25.359 1.00 12.32
ATOM 71 CA ARG 10 26.217 13.615 22.008 1.00 12.35
TER
ENDMDL