Hello all, I am working with a PDB file that contains a protein molecule (chain id A) and three different ligands in its binding site (as chains B, C and D). This file was made by combining three superimposed complex structures to illustrate the relationsips between the modes of binding of the different ligands.
I used PyMol and the following script to create an overview figure: ----[ PyMol script ]----------------------------------------- # Load the PDB file containing all the elements load combination.pdb # Separate structure into different objects # chain A is the protein create lectin,(A//) # chains B,C and D contain three different ligands create one,(B//) create two,(C//) create three,(D//) # delete the original structure delete combination # Set view hide lines,all zoom one,3 # set orientation,... # Color atoms according to functon color white,lectin # site 1 color green,(/lectin///85,86,106,132,138,220/) # site 2 color bluegreen,(/lectin///104,45/) # Generate van der Waals surface show surface,lectin # Ligands in different colors set stick_radius,0.05 color magenta,one show sticks,one color yellow,two show sticks,two color red,three show sticks,three ---------------------------------------------------------------- This works very well. Maybe a wizard could be created to automatically split a structure into separate objects for the different chains? -- Lieven Buts Vrije Universiteit Brussel
