Protein viewer Pymol
http://pymol.sourceforge.net/ is an excellent and widely applied protein
structure viewer. It has been developed by Warren Delano and
many tools and scripts are added by the scientific community.
Residue selections: Dragging the mouse over a part of
the amino acid sequence in the STRAP alignment creates a
residue selection in Pymol.
The STRAP cursor position refers to another Pymol selection.
Users can refer to these selections to show [S] or hide
[H] representations of residues like sphere,
cartoon or stick.
For example to show all atoms of the amino acid at the current cursor position as spheres
open the corresponding [S] menu of the selection "cursor" and select "spheres".
Removing a protein from Pymol: If a protein
would be removed in Pymol this would be unnoticed by STRAP.
Therefore it is recommended to use the STRAP user interface and not the Pymol user interface to remove proteins.
There are two possibilities:
- The STRAP menu item [Menu-bar>Protein>3D>View 3D-Structure]
- The STRAP object tree which is visible at the left of the STRAP application frame in advanced user mode.
Pymol commands:
Pymol commands (see http://pymol.sourceforge.net/newman/ref/S1000comref.html) are typed directly into the Pymol-window.
Most important commands:
- reset
Zooms the window and clipping planes to cover all objects.
- ray
Creates a ray-traced image of the current frame.
- png my_file.png
Writes an image file.
- bg white
White background.
- delete myProtein
Deletes an object. Understands wildcard
Related links: http://www.rubor.de/bioinf/
http://www.rubor.de/anlagen/PyMOL_Tutorial.pdf
