Re: [PyMOL] appending states to objects

[Kristian Rother <kristian.rother@ch...>]

Am Donnerstag, 17. Juli 2003 23:05 schrieb Vajdos, Felix:
> Is there a way to append states to objects within pymol?
>
> Here's the scenario:
> Now, each animation is 50 frames (states) long, and runs fine.  What I
> would like to do is at the end of each animation sequence to simply hav=
e
> the final state rock back and forth, as in with the "rock" button on th=
e
> Tcl window. However, I do not want to have the whole thing rocking duri=
ng
> the animation.

Dear Felix,

Though it may sound a little like advertisement, i recommend the rTools=20
package for PyMOL. (http://www.rubor.de/bioinf). =20
Here, you can issue some commands assigning states to frames, like

mvRot 1-500:1-50,z,90
mvRot 501-1000:50-1,z,-90
Which will let states 1 to 50 be shown across the first 500 frames (howev=
er,=20
state 50 is shown only in the last frame). In the second 500 frames, the=20
order is reversed, i.e. the sequence plays backwards.

You can also simply assign commands to frames, leaving the state untouche=
d:
mvSinmove 1001-1100,x,10
mvSinset 1001,1100,transparency,0.0,1.0

To play the animation, just type:
movie

And yes, you can get the structure rocking with these commands.
I apologize it does not run perfectly yet, as a bugfix release of rTools =
is=20
about to appear within a week.

I hope that was not too confusing,

Kristian

[PyMOL] appending states to objects

[Vajdos, Felix <felix_vajdos@gr...>]

Is there a way to append states to objects within pymol?

Here's the scenario:

I have 3 separate animation sequences all showing different structural
changes.  I've created all the necessary input files to generate the three
movies in exactly the same reference frame (relative to each other--i.e.
they all overlap).  

Now, each animation is 50 frames (states) long, and runs fine.  What I would
like to do is at the end of each animation sequence to simply have the final
state rock back and forth, as in with the "rock" button on the Tcl window.
However, I do not want to have the whole thing rocking during the animation.


I've looked through the manual, and I can't quite understand how to do this
to an existing state.  Ultimately, I want to write out the rendered images
to compile into an animated GIF for a colleague's PowerPoint presentation.  

Any suggestions would be appreciated.

Best regards,
Felix

Felix Vajdos
Research Scientist
Pfizer Inc
Eastern Point Road
Groton, CT  06340

860-715-6504



LEGAL NOTICE
Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.

RE: [PyMOL] appending states to objects

[Warren L. DeLano <warren@de...>]

Felix,

	You could do this by appending a rock command onto the last
frame of the animation:  Assuming the animation is 50 frames long...

   mappend 50: mstop; rock 1

should stop the movie and turn on rocking at the end of the animation.

   mappend 1: rock 0

would also stop rocking at the beginning of the animation.

Cheers,
Warren

--
mailto:warren@...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pymol-users-admin@... [mailto:pymol-users-
> admin@...] On Behalf Of Vajdos, Felix
> Sent: Thursday, July 17, 2003 1:05 PM
> To: 'pymol-users@...'
> Subject: [PyMOL] appending states to objects
> 
> Is there a way to append states to objects within pymol?
> 
> Here's the scenario:
> 
> I have 3 separate animation sequences all showing different structural
> changes.  I've created all the necessary input files to generate the
three
> movies in exactly the same reference frame (relative to each
other--i.e.
> they all overlap).
> 
> Now, each animation is 50 frames (states) long, and runs fine.  What I
> would
> like to do is at the end of each animation sequence to simply have the
> final
> state rock back and forth, as in with the "rock" button on the Tcl
window.
> However, I do not want to have the whole thing rocking during the
> animation.
> 
> 
> 
> I've looked through the manual, and I can't quite understand how to do
> this
> to an existing state.  Ultimately, I want to write out the rendered
images
> to compile into an animated GIF for a colleague's PowerPoint
presentation.
> 
> Any suggestions would be appreciated.
> 
> Best regards,
> Felix
> Felix Vajdos
> Research Scientist
> Pfizer Inc
> Eastern Point Road
> Groton, CT  06340
> 
> 860-715-6504
> 
> 
> 
> LEGAL NOTICE
> Unless expressly stated otherwise, this message is confidential and
may be
> privileged. It is intended for the addressee(s) only. Access to this
E-
> mail by anyone else is unauthorized. If you are not an addressee, any
> disclosure or copying of the contents of this E-mail or any action
taken
> (or not taken) in reliance on it is unauthorized and may be unlawful.
If
> you are not an addressee, please inform the sender immediately.
> 
> 
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Re: [PyMOL] appending states to objects

[Kristian Rother <kristian.rother@ch...>]

Am Donnerstag, 17. Juli 2003 23:05 schrieb Vajdos, Felix:
> Is there a way to append states to objects within pymol?
>
> Here's the scenario:
> Now, each animation is 50 frames (states) long, and runs fine.  What I
> would like to do is at the end of each animation sequence to simply hav=
e
> the final state rock back and forth, as in with the "rock" button on th=
e
> Tcl window. However, I do not want to have the whole thing rocking duri=
ng
> the animation.

Dear Felix,

Though it may sound a little like advertisement, i recommend the rTools=20
package for PyMOL. (http://www.rubor.de/bioinf). =20
Here, you can issue some commands assigning states to frames, like

mvRot 1-500:1-50,z,90
mvRot 501-1000:50-1,z,-90
Which will let states 1 to 50 be shown across the first 500 frames (howev=
er,=20
state 50 is shown only in the last frame). In the second 500 frames, the=20
order is reversed, i.e. the sequence plays backwards.

You can also simply assign commands to frames, leaving the state untouche=
d:
mvSinmove 1001-1100,x,10
mvSinset 1001,1100,transparency,0.0,1.0

To play the animation, just type:
movie

And yes, you can get the structure rocking with these commands.
I apologize it does not run perfectly yet, as a bugfix release of rTools =
is=20
about to appear within a week.

I hope that was not too confusing,

Kristian