3d visualization via RasMol program.
The rasmol tool is a wrapper on the RasMol visualization program. RasMol is open source software and runs on many platforms. The link above is for the Open Rasmol WWW site, not the Protein Explorer WWW site. Protein Explorer is a derivative of RasMol and runs primarily on Windows machines within a browser. This Pizza.py tool wraps the original RasMol program, not Protein Explorer.
The rasmol constructor takes a pdbfile object as its argument which produces PDB files that RasMol reads in. The pdbfile object can produce PDB files from a LAMMPS dump or data file, as well as in other ways.
The show() method runs RasMol on the atoms of snapshot N (converted to a PDB file) and displays the resulting image stored as image.gif. Either a default RasMol script or one you specify is used to format the RasMol image. The all() method loops thru all selected snapshots and runs RasMol on each one. The resulting image files are saved to image0000.gif, image0001.gif, etc. The prefix "image" can be changed via the file setting.
A RasMol script can be created by running RasMol itself (outside of Pizza.py), typing commands or choosing menu options to format the display as desired, then typing "write script filename". Alternatively the run() method will do this for you. It runs RasMol on snapshot N and lets you interact with RasMol directly either via typing or mouse operations in the RasMol window. When you type "quit" or "exit" the script file will be saved (do not exit via the Rasmol menu).
r = rasmol(p) create RasMol wrapper for pdb object p
r.file = "image" file prefix for created images (def = "image")
r.show(N) show snapshot at timestep N with default script r.show(N,"my.rasmol") use file as RasMol script
r.all() make images of all selected snapshots with def script r.all("my.rasmol") use file as RasMol script
r.run(N) run RasMol interactivly on snapshot N r.run(N,"new.rasmol") adjust via mouse or RasMol commands r.run(N,"new.rasmol","old.rasmol") type quit to save RasMol script file
if 2 args, 2nd arg is new script file, else save to "tmp.rasmol" if 3 args, 3rd arg is initial script file, else use default script
dump, gl, pdbfile, raster, svg
The RasMol program.