Protein viewers, Pymol, Jmol

[Menu-bar>View]
Comparing different 3D-viewers
* JMOL * RASMOL * PYMOL * VMD
Installed by STRAP allways Linux Linux, Windows, Mac never
Operation system all Linux, Unix all Linux, Unix
Performance medium high high with accelerated video cards very high
Memory consumption high low medium medium
# models per view 1 1 many many
Scripting language Rasmol scripting language Rasmol scripting language Python TCL, Python
Number of atom selections 1 1 many many
Shows superimposed proteins no no yes no
Move cursor to picked residue yes yes yes no

Protein PDB structure viewers are used for detailed 3D-visualization. Depending on the protein viewer the alignment pane and the 3D-view are interoperable.

Communication objects: Loading a protein into a protein structure viewer creates a communication object which is found under the respective protein node in the object tree. A context menu can be opened.

Simple residue selection: When the mouse is dragged over the sequence in the multiple alignment view the resulting selection will also be shown in the 3D-viewer. In the 3D-viewer the rendering style of the selected amino acids can be changed.

Interpreting commands: A major advantage of running a protein structure viewer from STRAP is that 3D-rendering commands can be stored in Modifying annotations.

Atom/Residue picking: When users pick an Atom in the 3D-view the alignment cursor jumps to the respective alignment position. This feature is implemented in most 3D-viewers. Related links: http://biodesign.asu.edu/labs/assets/lindsay/molvis/MOL.html