[Proteopedia] Expand selection to residues

Eric Martz emartz at microbio.umass.edu
Wed May 2 14:46:55 EDT 2012


A (small) new capability has been added to the Scene Authoring Tools 
in Proteopedia, in the "selections" tab, in the box "select within distance".

Up until now, you could "select atoms within [some number you 
specify] Angstroms of current selection".

The new capability is "Expand selection to include entire residues 
containing any selected atoms."

For example, consider a protein with a bound ligand, such as trypsin 
bound to an inhibitor, 1cbx.

Until now, you could show atoms within 4 Angstroms of ligand as 
balls. Now, in addition, you can show the amino acids containing 
those ligand-contacting atoms as sticks. In the Scene Authoring Tools:

1. load 1cbx, check selection halos.

2. selections: select residue type BZS (or mouse click selects 
residue/group, click on inhibitor)

3. selections: select atoms within 4 Angstroms of current selection.

4. selections: expand selection to entire residues containing any 
selected atoms.

5. selections: type BZS in "limit to residue types" and click "remove 
from selection". Now you have selected residues containing any atom 
within 4 Angstroms of the inhibitor, but not the inhibitor BZS.

6. representations: sticks

7. colors: elements

8. selections: select BZS again, and atoms with 4 Angstroms again, 
remove BZS from selection again.

9. representations: spacefill 40% to make medium-sized balls.

OPTIONAL: color ligand-contacting water oxygens magenta:

10. selections: all protein, remove from selection. This leaves 
selected only the non-protein atoms that contact the ligand, namely water.

11. colors: click on a magenta square.

See the result at
http://www.proteopedia.org/wiki/index.php/Sandbox

If it is not there, use the History tab to view the page as of May 2, 
2012 (by Student).

-Eric



----
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://Martz.MolviZ.Org

Proteopedia.Org Administrator
http://www.proteopedia.org/wiki/index.php/User:Eric_Martz 



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