VMDTricks
((short description what this page is about))
enable live update of secondary structure assigment
When selecting the Catoon or
NewCartoon representation, the secondary
structure elements are drawn such that they represent the structure in the
pdb file (first frame). When the secondary structure changes in a
trajectory, it is convenient to redraw the secondary structure
elements such that they represent the secondary structure of the
current frame.
To enable this behaviour add the following lines to the VMD statup file
~/.vmdrc
proc update_secondary_structure_assigment { args } {
foreach molid [molinfo list] {
mol ssrecalc $molid
}
}
trace variable vmd_frame(0) w update_secondary_structure_assigment
adding keyboard shortcuts
E.g. change graphical representation of top molecule to
NewCartoon,
when F1 is pressed.
user add key F1 { mol modstyle 0 0 NewCartoon }
creating multiple graphical representations of same molecule in script
mol modselect 0 top "protein"
mol modstyle 0 top NewCartoon
mol modcolor 0 top Chain
# add a second representation
mol addrep top
mol modselect 1 top "water"
mol modstyle 1 top Licorice
mol modcolor 1 top ColorID 1