Protein viewer Pymol
is a widely applied protein
structure viewer by Warren Delano.
Residue selections: Dragging the mouse over a part of
the amino acid sequence in the STRAP alignment creates a
residue selection in Pymol.
The alignment cursor position refers to another Pymol selection named "cursor".
Users can refer to these selections in Pymol. Using the [S]show or hide [H]hide menus in the side panel
of Pymol the representations of the selected atoms can be specified like sphere, cartoon or
stick.
Menu The generic 3D-menu for the Pymol view is opened by clicking the Pymol button which
will appear in a separate small panel which also acts as a drop target for further 3D-structures.
Related links: http://www.rubor.de/bioinf/
http://www.rubor.de/anlagen/PyMOL_Tutorial.pdf
Bugs:
Pymol does not treat negative pdb residue numbers correctly.
Pymol selection is unspecific if the chain identifier is a space character ' ';