OK. I can see a  bit clearer now :)
 
Yet which leads me to another question. About the group selection analysis below:
 
Select group for analysis
Group 0 ( System) has 2616 elements
Group 1 ( Protein) has 2470 elements
Group 2 ( Protein-H) has 2470 elements
Group 3 ( C-alpha) has 314 elements
Group 4 ( Backbone) has 934 elements
Group 5 ( MainChain) has 1246 elements
Group 6 ( MainChain+Cb) has 1540 elements
Group 7 ( MainChain+H) has 1246 elements
Group 8 ( SideChain) has 1224 elements
Group 9 ( SideChain-H) has 1224 elements
Group 10 ( Prot-Masses) has 2470 elements
Group 11 ( non-Protein) has 146 elements
Group 12 ( Ion) has 2 elements
Group 13 ( CL) has 2 elements
Group 14 ( Water) has 144 elements
Group 15 ( SOL) has 144 elements
Group 16 ( non-Water) has 2472 elements
Group 17 ( Water_and_ions) has 146 elements
 
What are those really? I don't have biology background really. All I know is that Protein (Secondary structure) has one or more chains and in it has
amino acids. And the protein consists of alpha helix and beta sheets. Basically my project is to plot contact map on the selected chain ( consisting alpha helix & beta sheets) of a protein.
I'm just a bit confused what are those groups for? I mean I don't really need those. I just need to plot on a chain.
 
Many thanks,
Suhaila
> Date: Mon, 19 Mar 2012 19:37:12 +0100
> Subject: Re: [PyMOL] Query on 'Select group for analysis' for Contact Map Visualizer Plugin
> From: tsjerkw@gmail.com
> To: bell_beauty12@hotmail.com
> CC: pymol-users@lists.sourceforge.net
>
> Hi Suheila,
>
> The CMV requires the contact map and the structure to match. So to get
> what you want, it's easiest to load the structure in pymol, and save
> only the part you want to analyze:
>
> save helix.pdb, ss h
> save sheet.pdb, ss s
>
> Then you can run g_mdmat on each of those, and load the result back in pymol.
>
> Hope it helps,
>
> Tsjerk
>
> On Mon, Mar 19, 2012 at 6:20 PM, Suhaila Haji Mohd Hussin
> <bell_beauty12@hotmail.com> wrote:
> > Hello especially for those who are experienced using Contact Map Visualizer
> > Plugin. About generating a contact map, after typing the following command
> > as shown:
> >
> > g_mdmat -f 2p31.pdb -s 2p31.pdb -mean contact-map.xpm
> >
> > It gives us a list of group selection to analyze such as below:
> >
> > Select group for analysis
> > Group 0 ( System) has 2616 elements
> > Group 1 ( Protein) has 2470 elements
> > Group 2 ( Protein-H) has 2470 elements
> > Group 3 ( C-alpha) has 314 elements
> > Group 4 ( Backbone) has 934 elements
> > Group 5 ( MainChain) has 1246 elements
> > Group 6 ( MainChain+Cb) has 1540 elements
> > Group 7 ( MainChain+H) has 1246 elements
> > Group 8 ( SideChain) has 1224 elements
> > Group 9 ( SideChain-H) has 1224 elements
> > Group 10 ( Prot-Masses) has 2470 elements
> > Group 11 ( non-Protein) has 146 elements
> > Group 12 ( Ion) has 2 elements
> > Group 13 ( CL) has 2 elements
> > Group 14 ( Water) has 144 elements
> > Group 15 ( SOL) has 144 elements
> > Group 16 ( non-Water) has 2472 elements
> > Group 17 ( Water_and_ions) has 146 elements
> >
> > My question is that is it possible to modify that group selection? I want to
> > add in group analysis on alpha helix & beta sheet.
> > For example Group 18 (Alpha helix) has 999 elements.
> >
> > If it is possible? How & where can I do that?
> >
> > Hope you reply a.s.a.p
> >
> > Many thanks,
> > Suhaila
> >
> > ------------------------------------------------------------------------------
> > This SF email is sponsosred by:
> > Try Windows Azure free for 90 days Click Here
> > http://p.sf.net/sfu/sfd2d-msazure
> > _______________________________________________
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands