Welcome everybody to the PyMOL mailing list. There are over 30
subscribers. I am very pleased that so many people want to use (and
thereby improve) the package.
> From: Ben Cornett
> Does anyone know how to get the size (pixels) of the viewer? I'd like
> to be able to write a python script that orients and colors a molecule
> and then renders it at whatever dpi I provide as a command-line
> argument.
Ben,
Hmm, not all of those features may exist yet, but the following will
help.
The "viewport" command can be used to change the window size.
Alternatively, the "ray" command can take width and height arguments.
Remember that two options exist for scripting: PyMOL commands and
Python. The former is easier for quick-and-dirty tasks.
# SCRIPT fig1.pml (PyMOL command language)
# RUN AS "pymol -c fig1.pml"
viewport 1024,768
load example.pdb
color marine
orient
ray
png fig1.png
# END
versus
# SCRIPT fig2.py (Python)
# RUN AS "pymol -c fig2.py"
from pymol import cmd
cmd.viewport(1024,768)
cmd.load("example.pdb")
cmd.color("marine")
cmd.orient()
cmd.ray()
cmd.png("fig2.png")
# END
also equivalent to
# SCRIPT fig3.pml (PyMOL)
# RUN AS "pymol -c fig3.pml"
load example.pdb
color marine
orient
ray 1024,768
png fig3.png
# END
Passing additional command arguments can't yet be done reliably, but you
might try playing around with -d (at least on unix). Note single quotes
and no spaces within the quote.
pymol -d 'w=1024;h=768'
should define "w" and "h" in the interpreter namespace.
Thus, the following works...
# SCRIPT fig3.py (Python)
# RUN AS "pymol -c -d 'w=1024;h=768' fig3.py "
from pymol import cmd
cmd.load("example.pdb")
cmd.color("marine")
cmd.orient()
cmd.ray(w,h)
cmd.png("fig3.png")
# END
You might even be able to pass in the input and output filenames:
pymol -c -d 'w=1024;h=768;i=example.pdb;o=fig4.png' fig4.py
# SCRIPT fig4.py (Python)
from pymol import cmd
cmd.load(i)
cmd.color("marine")
cmd.orient()
cmd.ray(w,h)
cmd.png(o)
# END
- Warren
