Dear All,
Thanks for all your suggestions on ray tracing the protein gallery.
In the end, I used several of the techniques suggested, and everything
worked out really well!
To summarize:
1. Use the grid_mode option (only available in the compiled from
source pymols)
2. Make a fake .pdb that has the corners and centers of a 3D box to
use for alignment
3. Use the set_view command to apply the same viewing matrix
4. Use the zoom command with a center and a distance specified.
Also, the cealign package is really helpful for aligning and
translating very dissimilar molecules.
Thanks! and all the best,
--Buz
On Dec 16, 2008, at 4:05 PM, DeLano Scientific wrote:
Hi Buz,
You can use "center" as a selection name for input with zoom, along
with a
distance value.
zoom center, distance
e.g.
# first, get the object you want in the center of the screen
orient
# then zoom the viewer by a fixed amount about the center point
zoom center, 10
# you may also wish to move the clipping planes in/out to avoid
cutting into
any of the molecular representations:
clip atoms, 4, selection=all
# also, depending upon the application, you might want to disable
perspective
set orthoscopic
# get rid of background pixels
unset opaque_background
# render
ray
# and save
save struct001.png
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com
-----Original Message-----
From: Buz Barstow [mailto:b...@mac.com]
Sent: Monday, December 15, 2008 11:42 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Ray Tracing A Protein Gallery
Dear All,
I'm making a gallery of protein molecules for my PhD thesis.
I'd like to find an automatic way to ensure that all of the
ray traced images have the same scale. Is there an easy way
to do this?
Thanks! and all the best,
--Buz
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