VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Mon Mar 07 2005 - 17:40:24 CST

Peter,

   James Stevens posted essentially the same question, but I forgot to send a solution to the general list. His post and my response precede your post below; from the first two, you should be able to extrapolate to your case.

Best,

Chris

___________________
James,

   You'll need two representations; one with "protein" or "chain A" as ribbon, and another with "chain A and resid 130 and not index 1 2 3" as bonds, where indices 1 2 and 3 are the atom indices for the carbonyl O, carbonyl C, and amide N of the backbone. If you use the Mouse/Label/Atoms tool with the second rep as just "chain A and resid 130" to start with, you can find these atom indices easily in the console window as you pick them.

Hope that helps,

Chris

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu]On Behalf
> Of James Stevens
> Sent: Friday, February 18, 2005 1:24 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l:
>
>
> Hi,
> Stupid question, but I would like to show a ribbon
> representation with
> specific side chains as bonds
> However, when I use:
> chain A and sidechain resid 130
> for example, I get the sidechain disconnected from the ribbon. Can
> anyone please tell me what the selection should be to include
> the bond
> to the CA atom of the mainchain.
>
> Best wishes
> James
>
>
_____________________
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu]On Behalf
> Of Peter Holm
> Sent: Monday, March 07, 2005 2:43 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: Display only side chains
>
>
> Dear list-readers,
> I wish to display only a selected set of residues created as
> a separate selection where the side chains are sticking out
> from the "new ribbons" object without main chain CO and NH
> disturbing the view. So I did the following selections:
>
> "residue 47 45 44 40 and not backbone"
>
> "residue 47 45 44 40 and alpha"
>
> This results in the view I wish to have when visualising the
> selection with licorice except that the Ca-Cb bond is
> missing. Any hints on how I can get the side chain visualised
> from Ca and "outwards" are most welcome and appreciated?
>
> Regards
>
> Peter
>
> ****************************************************
> Peter Holm, Ph.D. Student
> Molecular Biophysics
> Center for Chemistry and Chemical Engineering
> Lund University
> P.O.B. 124
> SE-22100 Lund
> SWEDEN
>
> Telephone numbers
> Office: +46-(0)46-2221448
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> E-mail: peter.holm_at_mbfys.lu.se
> http://www.mbfys.lu.se
> ****************************************************
>
>
>