[Molvis-list] help: SS-bond in Rasmol-2.7.3

[Herbert J. Bernstein]

From the RasMol manual, which is available online at www.rasmol.org:

SSBonds

Syntax:  ssbonds {<boolean>}
         ssbonds <value>

The RasMol

ssbonds

command is used to represent the disulphide bridges of the protein
molecule as either dotted lines or cylinders between the connected
cysteines. The first time that the ssbonds command is used, the program
searches the structure of the protein to find half-cysteine pairs
(cysteines whose sulphurs are within 3 Angstroms of each other) and
reports the number of bridges to the user. The command

ssbonds on

displays the selected bonds as dotted lines, and the command

ssbonds off

disables the display of ssbonds in the currently selected area. Selection
of disulphide bridges is identical to normal bonds, and may be adjusted
using the RasMol

set bondmode

command. The colour of disulphide bonds may be changed using the

colour ssbonds

command. By default, each disulphide bond has the colours of its connected
atoms.

By default disulphide bonds are drawn between the sulphur atoms within the
cysteine groups. By using the

set ssbonds

command the position of the cysteine's alpha carbons may be used instead.


=====================================================
 Herbert J. Bernstein, Professor of Computer Science
   Dowling College, Kramer Science Center, KSC 121
        Idle Hour Blvd, Oakdale, NY, 11769

                 +1-631-244-3035
                 yaya at dowling.edu
=====================================================

On Tue, 14 Mar 2006, Nanjiang Shu wrote:

> Hello,
>
>    I have a question about the ssbond function in Rasmol.
>
>    For protein with PDB code "1AOL", when typing SS-bond, it shows there
> are 6
>    SS bridges, and the distance between bonded sulfur atoms is around 2 Å.
>    However, both PDB file and DSSP file do not indicate there are any
> SS-bonds
>    for that protein. What scheme does Rasmol use to determine whether
> there is
>    an SS-bond or not? Something other than DSSP and PDB file?
>
> Thanks very much.
>
> Yours sincerely,
> Nanjiang S
>
> ------------------------------
> Nanjiang Shu, PhD
> Structural Chemistry
> Stockholm University
> Sweden
>
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