[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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