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78 lines
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HTML
78 lines
3.0 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py WWW Site</A> - <A HREF = "Manual.html">Pizza.py Documentation</A> - <A HREF = "Section_tools.html">Pizza.py Tools</A>
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</CENTER>
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<HR>
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<H3>rasmol tool
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</H3>
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<P><B>Purpose:</B>
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</P>
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<P>3d visualization via RasMol program.
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</P>
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<P><B>Description:</B>
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</P>
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<P>The rasmol tool is a wrapper on the <A HREF = "http://www.openrasmol.org">RasMol</A>
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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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</P>
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<P>The rasmol constructor takes a <A HREF = "pdbfile.html">pdbfile</A> 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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</P>
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<P>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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</P>
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<P>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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</P>
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<P><B>Usage:</B>
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</P>
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<PRE>r = rasmol(p) create RasMol wrapper for pdb object p
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</PRE>
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<PRE>r.file = "image" file prefix for created images (def = "image")
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</PRE>
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<PRE>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
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</PRE>
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<PRE>r.all() make images of all selected snapshots with def script
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r.all("my.rasmol") use file as RasMol script
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</PRE>
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<PRE>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
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</PRE>
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<PRE> 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
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</PRE>
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<P><B>Related tools:</B>
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</P>
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<P><A HREF = "dump.html">dump</A>, <A HREF = "gl.html">gl</A>, <A HREF = "pdbfile.html">pdbfile</A>,
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<A HREF = "raster.html">raster</A>, <A HREF = "svg.html">svg</A>
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</P>
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<P><B>Prerequisites:</B>
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</P>
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<P>The RasMol program.
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</P>
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</HTML>
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