I see!

Many thanks  Tsjerk! XD

> Date: Mon, 19 Mar 2012 20:59:08 +0100
> Subject: Re: [PyMOL] Query on 'Select group for analysis' for Contact Map Visualizer Plugin
> From: tsjerkw@gmail.com
> To: bell_beauty12@hotmail.com
>
> Hi Suheila,
>
> These groups are for selecting specific subgroups of a protein or of
> the solvent. But they don't seem to be important for what you want to
> do. Just choose 'protein'.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Mar 19, 2012 at 7:58 PM, Suhaila Haji Mohd Hussin
> <bell_beauty12@hotmail.com> wrote:
> >
> >  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
> >> >
> >> >
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> >>
> >>
> >>
> >> --
> >> 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
>
>
>
> --
> 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