hy (NIH/NCI) [C] via PyMOL-users
Reply: Waybright, Timothy (NIH/NCI) [C]
Date: May 12, 2020 at 6:43:54 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Scenes
Hello,
I am looking at a protein with a nucleotide. I want to see what happens when a
residue close to the nucleot
Hello,
I am looking at a protein with a nucleotide. I want to see what happens when a
residue close to the nucleotide (or far away) is changed via Mutagenesis to
another residue. When I store scenes from the initial views, they are fine -
they have the 'old' residue in the positions I want th
[responding to Folmer Fredslund, private message]
Thanks, Folmer. What I was missing was the difference between
color colorName, selection
and
set xxx_color, colorName
and
set xxx_color, colorName, selection
Each of which does something totally different internally in PyMOL. I see
now
I guess I still don't understand exactly what a scene is:
"scene" saves and restores scenes. A scene consists of the camera
view, all object activity information, all atom-wise visibilities,
all atom-wise colors, all representations, the global frame index,
and may contain a text
Hi Bob,
it's the object-level "state" setting:
fetch 1nmr 1d7q, async=0
set state, 3, 1nmr
set state, 10, 1d7q
And since scenes do not store settings, this cannot be stored with a scene.
Cheers,
Thomas
On Jun 3, 2013, at 10:41 AM, Robert Hanson wrote:
> [[sorry -- not used to a list that r
[[sorry -- not used to a list that requires "reply-all" to go back to the
list]]
What you describe there is a way to load a specific file into a specific
state, I think. I meant, once you have a set of multi-state objects, can I
select to compare two different states, one from one and one from th
Hi Bob,
The answer is yes to all.
fetch 1ubq, state=3
fetch 6lzm, state=10
cmd.load_cgo([7.0,0,0,0,2],name="sphere",state=2)
The representations (e.g. surface) do have states in the sense that the
each state gives a different surface. But whether the surface is shown or
not is controlled globall
Questions:
Can two objects be in two different states -- object1 in state 3 and
object2 in state 10, for instance, at the same time? If so, how is that set
up? How is that then incorporated into a scene?
Do CGO, measurements, mesh, and volume objects have states as well?
Bob
--
Robert M. Hanso
> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
> Of Richard Baxter
> Sent: Tuesday, February 19, 2008 12:50 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] scenes and animate v
Dear All,
I can make scenes and store them, but I do not understand how to us the
animate or other commands to make a movie by moving from one scene to
the next.
I have made a simple movie with frames and mdo, but I am not sure how to
us a command (mmatrix?) to associate a particular set_view wit
; [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Nat Echols
> Sent: Saturday, October 29, 2005 3:59 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] scenes and movies
>
>
> Apologies if this has been asked/answered already. My
> rotation student jus
Apologies if this has been asked/answered already. My rotation student
just showed me how PyMOL animates the transition between scenes, which
makes for some beautiful zooming effects. Is it possible to capture these
in a movie?
thanks,
Nat
Hi Chris,
I've been using this function a lot in my teaching. You don't need to
convert it to a movie, just save session as a .psw (pymol show file)
with the scenes embedded in there. Then from within powerpoint just set
up a hyperlink (Insert hyperlink) and point it to the .psw file. In
pre
Hi All,
I'm using Pymol 0.98 on a mac G5. I've created a number of scenes
using the append command and would like to convert these scenes to a
format suitable for a powerpoint presentation. I've tried in vain to
make a movie which plays through these scenes using mset and mdo with
no succes
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