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73 lines
2.7 KiB
Plaintext
73 lines
2.7 KiB
Plaintext
"Pizza.py WWW Site"_pws - "Pizza.py Documentation"_pd - "Pizza.py Tools"_pc :c
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:link(pws,http://www.cs.sandia.gov/~sjplimp/pizza.html)
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:link(pd,Manual.html)
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:link(pc,Section_tools.html)
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:line
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rasmol tool :h3
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[Purpose:]
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3d visualization via RasMol program.
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[Description:]
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The rasmol tool is a wrapper on the "RasMol"_http://www.openrasmol.org
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visualization program. RasMol is open source software and runs on
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many platforms. The link above is for the Open Rasmol WWW site, not
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the Protein Explorer WWW site. Protein Explorer is a derivative of
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RasMol and runs primarily on Windows machines within a browser. This
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Pizza.py tool wraps the original RasMol program, not Protein Explorer.
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The rasmol constructor takes a "pdbfile"_pdbfile.html object as its
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argument which produces PDB files that RasMol reads in. The pdbfile
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object can produce PDB files from a LAMMPS dump or data file, as well
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as in other ways.
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The show() method runs RasMol on the atoms of snapshot N (converted to
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a PDB file) and displays the resulting image stored as image.gif.
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Either a default RasMol script or one you specify is used to format
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the RasMol image. The all() method loops thru all selected snapshots
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and runs RasMol on each one. The resulting image files are saved to
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image0000.gif, image0001.gif, etc. The prefix "image" can be changed
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via the file setting.
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A RasMol script can be created by running RasMol itself (outside of
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Pizza.py), typing commands or choosing menu options to format the
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display as desired, then typing "write script filename".
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Alternatively the run() method will do this for you. It runs RasMol
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on snapshot N and lets you interact with RasMol directly either via
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typing or mouse operations in the RasMol window. When you type "quit"
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or "exit" the script file will be saved (do not exit via the Rasmol
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menu).
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[Usage:]
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r = rasmol(p) create RasMol wrapper for pdb object p :pre
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r.file = "image" file prefix for created images (def = "image") :pre
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r.show(N) show snapshot at timestep N with default script
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r.show(N,"my.rasmol") use file as RasMol script :pre
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r.all() make images of all selected snapshots with def script
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r.all("my.rasmol") use file as RasMol script :pre
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r.run(N) run RasMol interactivly on snapshot N
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r.run(N,"new.rasmol") adjust via mouse or RasMol commands
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r.run(N,"new.rasmol","old.rasmol") type quit to save RasMol script file :pre
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if 2 args, 2nd arg is new script file, else save to "tmp.rasmol"
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if 3 args, 3rd arg is initial script file, else use default script :pre
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[Related tools:]
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"dump"_dump.html, "gl"_gl.html, "pdbfile"_pdbfile.html,
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"raster"_raster.html, "svg"_svg.html
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[Prerequisites:]
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The RasMol program.
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