VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Mon Jan 28 2002 - 11:32:36 CST

The default radius for P and O atoms is 1.5 and 1.3, respectively (PSF files
can override these values). VMD draws a bond when the two atoms are within
0.6 * (r1 + r2). In this case that would be 1.68. Note that I'm basing my
comments on a reading of the code; I haven't actually tried this.

The VMD User's Guide has more information on how you can customize the bonds
in a molecule using the atomselect Tcl command.

Justin

On Mon, Jan 28, 2002 at 12:26:27PM +0100, Vlad Cojocaru wrote:
> Hello!
> Does somebody know at what distance a bond P-O5' from the DNA backbone
> is broken by VMD?
>
> --
> Vlad Cojocaru
> Max Planck Institut for Biophysical Chemistry
> Deparment: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1389
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> vcojoca_at_gwdg.de
> Home Address: Gutenbergstrasse 26/8
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-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
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