Re: [PyMOL] Delete frames in movie
Hi Matthias, there is 'mdelete', 'madd' and 'minsert'. PyMOL>madd ? Usage: madd [ specification [, frame [, freeze ]]] PyMOL>mdelete ? Usage: mdelete [ count [, frame [, freeze [, object PyMOL>minsert ? Usage: minsert count [, frame [, freeze [, object]]] Cheers, Thomas Matthias Schmidt wrote, On 07/09/11 22:32: > Hi, > > I made a nice movie and it's fine and I would just like to delete a > part of it or to insert some frames. How is that possible? Mset resets > the whole movie and mview does not seem to do what I would like it to > do... > > Best, > > Matthias -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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] PYMOL MOVIE
Dear MfG, formerly known as Holfelder, here's an expanded script:
load x_1.pdb
zoom
#orient molecule at this point as you desire
ray
png x_1
disable x_1
for i in range (2,10001): \
cmd.load("x_%d.pdb" %i) \
cmd.super("x_%d" %i, "x_1") \
cmd.ray() \
cmd.png("x_%05d" %i) \
cmd.disable("x_%d" %i) # or cmd.delete("x_%d" %i)
If you put the script into a file and load the orientation of the first
molecule before the first ray-tracing, you can execute it remotely
without the interface on the fastest machine (pymol -qc script.py).
This will be much quicker. Assemble the png files into a movie with
Quicktime Pro or Adobe Premier or mencoder (see PyMOL Wiki).
Andreas
On 10/07/2011 6:18, Babban Mia wrote:
> Thanks a lot Andrea and Michael
>
> So this would align/super impose all the other pdbs wrt the first PDB.
> How Do I make a movie of that ?
>
> Please advise
> I want to be able to show this "blob" of structures(obtained after
> aligning) from different angles and by rotation.
>
> I guess I would use the mset command,Would it work ?
>
> Please also show me how to incorporate the zoom command in the python
> script so that the structures look well small and not enlarged and extended.
>
>
> Danke!
>
> MfG
>
--
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Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
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Re: [PyMOL] PYMOL MOVIE
Just a little bit of a further note on top of what Andreas said. If you are
doing all of the commands from a script you might want to cmd.disable() the
first molecule so that you can align to it, but not see it in the
animation. Then you can delete each molecule (after 1) after you've used
it.
2011/7/10 Andreas Förster
> Holfelder!
>
> I don't see your doubts. Your first point's a guess - and you're right
> - and the second one a questions.
>
> Before I answer, one warning: If you have 1 pdb files and numbering
> starts at 1, the last one will be 1, not like you say. Be
> aware of what you have.
>
> for i in range (1,10001): \
> cmd.load("x_%d.pdb" %i) \
> cmd.super("x_%d" %i, "x_1")
>
> Will load 1 files and superpose every structure onto the first. The
> curious % notation substitutes a variable into a string. The load loads
> files and super superposes one structure onto another.
>
> Hope that helps.
>
>
> Andreas
>
>
>
> On 10/07/2011 12:05, Babban Mia wrote:
> > Hello Everyone
> >
> > I have got a doubt relating to making PYMOL MOVIE.
> > I have like 10,000 PDBs named x_1.pdb .x_23.pdb and so on
> >
> > I want to make a movie which essentially should act as the slideshow
> > from x_1.pdb to . x_.pdb
> >
> > This would show,kind of show the MD simulations for the protein.
> >
> > DOUBTS :
> >
> > 1 . I guess I would have to align the pdbs wrt some source to actually
> > be able to see the real MD changes in the succeeding pdb structures.
> > 2. Please show me some commands on how I can achieve all of above.
> >
> > Thanks again
> >
> > Best
> >
> > Holfelder
> >
> >
> >
> >
> --
> > All of the data generated in your IT infrastructure is seriously
> valuable.
> > Why? It contains a definitive record of application performance, security
> > threats, fraudulent activity, and more. Splunk takes this data and makes
> > sense of it. IT sense. And common sense.
> > http://p.sf.net/sfu/splunk-d2d-c2
> >
> >
> >
> > ___
> > 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
>
> --
> Andreas Förster, Research Associate
> Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
> http://www.msf.bio.ic.ac.uk
>
>
> --
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
> ___
> 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
>
--
Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University
--
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2___
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Re: [PyMOL] PYMOL MOVIE
Holfelder!
I don't see your doubts. Your first point's a guess - and you're right
- and the second one a questions.
Before I answer, one warning: If you have 1 pdb files and numbering
starts at 1, the last one will be 1, not like you say. Be
aware of what you have.
for i in range (1,10001): \
cmd.load("x_%d.pdb" %i) \
cmd.super("x_%d" %i, "x_1")
Will load 1 files and superpose every structure onto the first. The
curious % notation substitutes a variable into a string. The load loads
files and super superposes one structure onto another.
Hope that helps.
Andreas
On 10/07/2011 12:05, Babban Mia wrote:
> Hello Everyone
>
> I have got a doubt relating to making PYMOL MOVIE.
> I have like 10,000 PDBs named x_1.pdb .x_23.pdb and so on
>
> I want to make a movie which essentially should act as the slideshow
> from x_1.pdb to . x_.pdb
>
> This would show,kind of show the MD simulations for the protein.
>
> DOUBTS :
>
> 1 . I guess I would have to align the pdbs wrt some source to actually
> be able to see the real MD changes in the succeeding pdb structures.
> 2. Please show me some commands on how I can achieve all of above.
>
> Thanks again
>
> Best
>
> Holfelder
>
>
>
> --
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security
> threats, fraudulent activity, and more. Splunk takes this data and makes
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2
>
>
>
> ___
> 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
--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk
--
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
___
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Re: [PyMOL] Delete frames in movie
Hey Matthias, for movie editing, you can use Adobe Premier, obviously. If you have an older version of Photoshop lying around (pre-CS3), you can use the bundled Image Ready for many simple movie-editing tasks. Avidemux also helps you remove and change frames in movies. All three work on a Mac, which also has its own movie editor that comes with the breathtaking marketing praise of any Apple product. Andreas On 09/07/2011 9:32, Matthias Schmidt wrote: > Hi, > > I made a nice movie and it's fine and I would just like to delete a > part of it or to insert some frames. How is that possible? Mset resets > the whole movie and mview does not seem to do what I would like it to > do... > > Best, > > Matthias > -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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
