I haven't tested, but the grid_mode should work, all you need to do is correct the underscore typo:
set grid_mode, 1 # without _
set grid_slot, 2, object2
set grid_slot, 1, object1

Picture size and quality is not controlled by viewport unless you are making a movie, in that case set viewport, ray_trace_frames and movie_quality:
#Then use either:
cmd.movie.produce('example.mpg',mode='ray', preserve=0, quality=100)

I your case, however, a single image is best made using png:

cmd.png('example.png', '15cm', '10cm', dpi=300, ray=1)

this will give you a 15x10 cm image at 300 dpi, regardless of viewport.

About starting in fullscreen:
using the command line option '-e' should make pymol start in fullscreen
this will probably not work with '-c', but you can open your script from another shortcut.

Hope this helps,


On Thu, Jun 19, 2014 at 5:33 AM, J.R. W <jwillis0720@gmail.com> wrote:

What I’d like to do is set_grid_mode_1, ray trace, and then output a png in batch mode (-c)

However if you code this in the .pml:

set_grid_mode, 1
set grid_slot, 2, object2
set grid_slot, 1, object1

viewport 1000,1000 #not sure how to get fullscreen this maybe OS specific

ray 1000,1000
png somepic.png

Grid mode does not show up in the picture and the viewport in the session is still the default window size. However, grid mode does work in the session. 

So my question(s) are this:

1. Can you use grid mode in batch mode scripts to output an image?
2. Can you encode a full screen GUI in the pymol session so when you open up the session, it is full screen?

Using MacPyMOL latest release, can switch to X11 if necessary.

Thanks so much!


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