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:

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

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

Many thanks,

Suhaila