date:20160307

Re: [PyMOL] How to store matrix settings for individual scenes?

2016-03-07 Thread Schubert, Carsten [JRDUS]

Hi Thomas,

Movie won't work since the session files are distributed and need to be 
interactive. I'll try Jared's solution, if that does not work could we treat 
this as an enhancement request?

Cheers,

Carsten

-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] 
Sent: Monday, March 07, 2016 2:51 PM
To: Schubert, Carsten [JRDUS]
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to store matrix settings for individual scenes?

Hi Carsten,

What's your use case? Since movie frames can store object matrices, would 
creating an actual movie solve your problem? Example of an animated 
superposition:

# get sample data
fetch 1hbb, async=0
split_chains
delete 1hbb

# set up movie frames
mset 1x100

# make "align" modify the motion matrix (but without # instant storing to 
current frame) set matrix_mode, 1 set movie_auto_store, 0

# store object matrices to frame 1
mview store, 1, object=*

# superpose structures and store matrices to frame 100 extra_fit mview store, 
100, object=*

# optional: add scenes
color blue
scene blue, store
color red
scene red, store
mview store, 1, scene=blue
mview store, 100, scene=red


If this doesn't fit your use case, I'd go with Jared's solution of an enhanced 
scene function.

Cheers,
  Thomas

On 07 Mar 2016, at 12:35, Schubert, Carsten [JRDUS]  
wrote:

> Yeah, but not my preferred choice. Tried to do this the elegant way, but 
> bumping up against Pymol's limits unless Thomas has a workaround.
>  
> From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu]
> Sent: Monday, March 07, 2016 12:15 PM
> To: Schubert, Carsten [JRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] How to store matrix settings for individual scenes?
>  
> Hi Carsten -
>  
> I'd probably create new objects and use those for superimposition, rather 
> than moving the originals.  That would leave your scenes intact.
>  
> Cheers,
> Jared
>  
> --
> Jared Sampson
> Columbia University
>  
> On Mar 7, 2016, at 12:10 PM, Schubert, Carsten [JRDUS]  
> wrote:
>  
> Hi,
>  
> I am trying to create a session file of a multimeric protein, in which each 
> monomer is displayed first using the original  matrix settings broken out 
> into individual scenes. After that all monomers are overlayed on top of each 
> other and the superposition matrices are copied and applied to the ligands, 
> etc. So far so good, however once the matrices are applied this also affects 
> the matrices for the scenes created previous to the overlay and matrix_copy. 
> Any way I can store the matrices in each scene instead of having them applied 
> globally once?
>  
> Cheers,
>  
> Carsten

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
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Re: [PyMOL] How to store matrix settings for individual scenes?

2016-03-07 Thread Thomas Holder

Hi Carsten,

What's your use case? Since movie frames can store object matrices, would 
creating an actual movie solve your problem? Example of an animated 
superposition:

# get sample data
fetch 1hbb, async=0
split_chains
delete 1hbb

# set up movie frames
mset 1x100

# make "align" modify the motion matrix (but without
# instant storing to current frame)
set matrix_mode, 1
set movie_auto_store, 0

# store object matrices to frame 1
mview store, 1, object=*

# superpose structures and store matrices to frame 100
extra_fit
mview store, 100, object=*

# optional: add scenes
color blue
scene blue, store
color red
scene red, store
mview store, 1, scene=blue
mview store, 100, scene=red


If this doesn't fit your use case, I'd go with Jared's solution of an enhanced 
scene function.

Cheers,
  Thomas

On 07 Mar 2016, at 12:35, Schubert, Carsten [JRDUS]  
wrote:

> Yeah, but not my preferred choice. Tried to do this the elegant way, but 
> bumping up against Pymol’s limits unless Thomas has a workaround.
>  
> From: Sampson, Jared M. [mailto:jms2...@cumc.columbia.edu] 
> Sent: Monday, March 07, 2016 12:15 PM
> To: Schubert, Carsten [JRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] How to store matrix settings for individual scenes?
>  
> Hi Carsten - 
>  
> I'd probably create new objects and use those for superimposition, rather 
> than moving the originals.  That would leave your scenes intact.
>  
> Cheers,
> Jared
>  
> --
> Jared Sampson
> Columbia University
>  
> On Mar 7, 2016, at 12:10 PM, Schubert, Carsten [JRDUS]  
> wrote:
>  
> Hi,
>  
> I am trying to create a session file of a multimeric protein, in which each 
> monomer is displayed first using the original  matrix settings broken out 
> into individual scenes. After that all monomers are overlayed on top of each 
> other and the superposition matrices are copied and applied to the ligands, 
> etc. So far so good, however once the matrices are applied this also affects 
> the matrices for the scenes created previous to the overlay and matrix_copy. 
> Any way I can store the matrices in each scene instead of having them applied 
> globally once?
>  
> Cheers,
>  
> Carsten

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
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Re: [PyMOL] Immediately crashing

2016-03-07 Thread Thomas Holder

Hi Joachim,

Are the graphics drivers (both Intel and AMD) up-to-date? Such crashes are 
almost always graphics driver related. Note that only one of the two graphics 
cards will be active for PyMOL, depending on your setup (performance vs. 
power-saving).

Cheers,
  Thomas

On 07 Mar 2016, at 11:05, Reichelt, Joachim  
wrote:

> Dear all,
> 
> I just got a used DELL LATITUDE 3540. It got an Intel and an AMD graphics at 
> 1605x1050.
> 
> I installed PyMOL-v1.8.0.6-Win32.msi.
> But on start there is only flash up the cmd windows and that it was. The MS 
> error dialog pops up.
> 
> So I tried PyMOL-v1.7.0.5-Win32.msi, but all the same.
> 
> 
> Mit freundlichen Grüßen
> 
> Joachim Reichelt
> 
> 
> 
> Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
> Braunschweig | www.helmholtz-hzi.de
> Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie"
> 50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50
> 
> Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
> Bundesministerium für Bildung und Forschung
> Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für 
> Wissenschaft und Kultur
> Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer
> Gesellschaft mit beschränkter Haftung (GmbH)
> Sitz der Gesellschaft: Braunschweig
> Handelsregister: Amtsgericht Braunschweig, HRB 477

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
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[PyMOL] Immediately crashing

2016-03-07 Thread Reichelt, Joachim

Dear all,

I just got a used DELL LATITUDE 3540. It got an Intel and an AMD graphics at 
1605x1050.

I installed PyMOL-v1.8.0.6-Win32.msi.
But on start there is only flash up the cmd windows and that it was. The MS 
error dialog pops up.

So I tried PyMOL-v1.7.0.5-Win32.msi, but all the same.


Mit freundlichen Grüßen

Joachim Reichelt









Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
Braunschweig | www.helmholtz-hzi.de
Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie"
50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50

Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
Bundesministerium für Bildung und Forschung
Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für 
Wissenschaft und Kultur
Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer
Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477
--
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://makebettercode.com/inteldaal-eval
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] How to store matrix settings for individual scenes?

Re: [PyMOL] How to store matrix settings for individual scenes?

Re: [PyMOL] Immediately crashing

[PyMOL] Immediately crashing

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