Hi Babban,
Expanding on what Andreas wrote, I would make a few modifications
given your request. The following code will load your PDBs into one
object, fit the states and setup an optimal view. Next the movie
will be 10 seconds long (300 frames) but will play through the 10000
states. Adjust your numbers and representation as necessary.
# load all the PDBs into one mult-state object
for i in range (1,10001): \
cmd.load("x_%d.pdb" %i, "myMD")
# fit all to the first state
intrafit MyMD
# after fitting, get largest view
orient
# smooth out high frequency vibrations
smooth
# create a blank movie over 300 frames
mset 1x300
# goto frame 1
frame 1
# store frame 1 in state 1
mview store, state=1
# goto frame 300
frame 300
# store frame 300 in state 10000;
# PyMOL will interpolate over the
# states for us.
mview store, state=10000
# go back to frame 1 and play
frame 1
mplay
A few notes:
* To show "the blob" of all states just use, "set all_states, 1".
* The mset command (http://pymolwiki.org/index.php/Mset)
* The mview command (http://pymolwiki.org/index.php/MovieSchool_2#mview)
* For more information on making movies in PyMOL, please check out
the Movieschool (http://pymolwiki.org/index.php/MovieSchool) tutorial
on the PyMOLWIki. It's a bit outdated but for the most part presents
the topics needed to make movies in PyMOL.
Cheers,
-- Jason
2011/7/10 Babban Mia <babban...@gmail.com>:
> 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
> 2011/7/10 Andreas Förster <docandr...@gmail.com>
>>
>> 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 10000 pdb files and numbering
>> starts at 1, the last one will be 10000, not 9999 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 10000 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_9999.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
>>>
>>>
>>>
>>>
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>>> All of the data generated in your IT infrastructure is seriously
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>>>
>>>
>>> _______________________________________________
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>>
>> --
>> 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
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
------------------------------------------------------------------------------
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
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