When I do the following
hide all
show sticks, all
scene 001, store
set_bond stick_transparency, 0.5, all
scene 002, store
scene 001
the stick_transparency setting is not restored. I was hoping I could use
scenes to slowly fade out a part of a molecule by adding several scenes
with increasing
I realized that the mdo command can be used to change the
stick_transparency setting.
mdo 1: set_bond stick_transparency, 0, all
mdo 100: set_bond stick_transparency, 0.8, all
and so on. I noticed that the example section in the help text for the
mdo command is incorrect. It states:
EXAMPLE
Hi Nick,
This is something Robert Campbell alluded to a few days ago. To get
what you want, the python block and mdo are you friends:
# create an ala fragment and setup the view
frag ala
as sticks
orient
# 60-frame movie
mset 1x60
# start a Python block that fades out the fragment
python
Thanks.
On 05/20/11 11:13, Jason Vertrees wrote:
Hi Nick,
This is something Robert Campbell alluded to a few days ago. To get
what you want, the python block and mdo are you friends:
# create an ala fragment and setup the view
frag ala
as sticks
orient
# 60-frame movie
mset
Hi list,
I'm trying to use PyMOL to construct an image of the total contiguous contact
surface that starts at a particular place on the surface of a protein, without
all the visual distraction and clutter that comes from other regions of the
protein surface (not to mention internal cavities).
I
The last time I tried to do something similar, I found HOLLOW (
http://hollow.sourceforge.net/) to be very useful. There's a nice tutorial
for showing a binding site, rather than an interior cavity, here:
http://hollow.sourceforge.net/binding.html .
Cheers,
-Michael
On Fri, May 20, 2011 at 7:11
