Re: [PyMOL] How to construct a view showing only a single contiguous cavity

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

[PyMOL] How to construct a view showing only a single contiguous cavity

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 s

Re: [PyMOL] mdo command

Hi Nick, Thanks, I'll update the code. Cheers, -- Jason On Fri, May 20, 2011 at 1:13 PM, Nicolas Bock wrote: > 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, a

Re: [PyMOL] store/recall stick_transparency in scene?

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 m

Re: [PyMOL] store/recall stick_transparency in scene?

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 pytho

[PyMOL] mdo command

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

[PyMOL] store/recall stick_transparency in scene?

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 st