Re: [PyMOL] Rotation of a Protein

[Thomas Holder]

Hi Kanika,

you can do this with the "rotate" command, without any additional script 
(like Michael already suggested). Note: for a dimer the the center of 
mass does not yet define an axis, my example uses an arbitrary axis on 
the mirror plane between the monomers.

# get some homodimer
fetch 3p8d, dimer, async=0

# create copies of one monomer
create copy1, dimer and chain A
create copy2, dimer and chain A
create copy3, dimer and chain A
create copy4, dimer and chain A

# orient will put the (unweighted) center of mass in the middle of
# the window and both monomers on the camera x-axis
orient dimer

# now rotate around the z-axis in camera space
rotate z, 60, copy1
rotate z, 120, copy2
rotate z, 180, copy3
rotate z, 240, copy4

Have a look at:
http://pymolwiki.org/index.php/Orient
http://pymolwiki.org/index.php/Rotate

If you need more fine control, go for Troels suggestion. There are also 
center-of-mass scripts on the PyMOLWiki.

Cheers,
   Thomas

kanika sharma wrote, On 10/09/11 07:47:
> I need to rotate the second unit of the dimeric protein on the line 
> joining their center of masses. rotate it at a atep of 60 degrees till 
> 240 degree..
> 
> 2011/10/8 Troels Emtekær Linnet  >
> 
> If you need rotations around an line, instead of axis, check out
> 
> http://www.pymolwiki.org/index.php/Rotkit
> 
> Troels Emtekær Linnet
> Karl-Liebknecht-Straße 53, 2 RE 
> 04107 Leipzig, Tyskland
> Mobil: +49 1577-8944752
> 
> 
> 
> 2011/10/7 kanika sharma  >
> 
> Hello everyone,
> I Have a protein with 2 chains.
> I have to rotate the second chain of the protein by
> 60,120,180,240 degrees each.
> Is there a script in PyMol that can do that?
> 
> Best,
> Kanika

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

--
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Re: [PyMOL] Rotation of a Protein

[Troels Emtekær Linnet]

Create two new molecules from the originial.
then

import rotkit
*rotateline Pos1=**atomcoordM1**, Pos2=atomcoordM2, degangle=60,
molecule=dim1*




2011/10/9 kanika sharma 

> I need to rotate the second unit of the dimeric protein on the line joining
> their center of masses. rotate it at a atep of 60 degrees till 240 degree..
>
>
> 2011/10/8 Troels Emtekær Linnet 
>
>> If you need rotations around an line, instead of axis, check out
>>
>> http://www.pymolwiki.org/index.php/Rotkit
>>
>> Troels Emtekær Linnet
>> Karl-Liebknecht-Straße 53, 2 RE 
>> 04107 Leipzig, Tyskland
>> Mobil: +49 1577-8944752
>>
>>
>>
>> 2011/10/7 kanika sharma 
>>
>>>  Hello everyone,
>>> I Have a protein with 2 chains.
>>> I have to rotate the second chain of the protein by 60,120,180,240
>>> degrees each.
>>> Is there a script in PyMol that can do that?
>>>
>>> Best,
>>> Kanika
>>>
>>>
>>> --
>>> 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-d2dcopy2
>>> ___
>>> 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
>>>
>>
>>
>
--
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Why? It contains a definitive record of application performance, security
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Re: [PyMOL] Rotation of a Protein

[kanika sharma]

I need to rotate the second unit of the dimeric protein on the line joining
their center of masses. rotate it at a atep of 60 degrees till 240 degree..

2011/10/8 Troels Emtekær Linnet 

> If you need rotations around an line, instead of axis, check out
>
> http://www.pymolwiki.org/index.php/Rotkit
>
> Troels Emtekær Linnet
> Karl-Liebknecht-Straße 53, 2 RE 
> 04107 Leipzig, Tyskland
> Mobil: +49 1577-8944752
>
>
>
> 2011/10/7 kanika sharma 
>
>> Hello everyone,
>> I Have a protein with 2 chains.
>> I have to rotate the second chain of the protein by 60,120,180,240 degrees
>> each.
>> Is there a script in PyMol that can do that?
>>
>> Best,
>> Kanika
>>
>>
>> --
>> 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-d2dcopy2
>> ___
>> 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
>>
>
>
--
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-d2dcopy2___
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Re: [PyMOL] Rotation of a Protein

[Troels Emtekær Linnet]

If you need rotations around an line, instead of axis, check out

http://www.pymolwiki.org/index.php/Rotkit

Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE 
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752



2011/10/7 kanika sharma 

> Hello everyone,
> I Have a protein with 2 chains.
> I have to rotate the second chain of the protein by 60,120,180,240 degrees
> each.
> Is there a script in PyMol that can do that?
>
> Best,
> Kanika
>
>
> --
> 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-d2dcopy2
> ___
> 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
>
--
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-d2dcopy2___
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Re: [PyMOL] Rotation of a Protein

[Michael Zimmermann]

# get a molecule with 2 chains
fetch 1t3r,async=0
# split it into two objects
create new1, polymer and chain a
create new2, polymer and chain b
delete 1t3r
# in the interface for new1, click: A -> movement -> deprotect
# now you can rotate it individually
rotate x,90,new1

On Fri, Oct 7, 2011 at 8:04 AM, kanika sharma  wrote:

> Hello everyone,
> I Have a protein with 2 chains.
> I have to rotate the second chain of the protein by 60,120,180,240 degrees
> each.
> Is there a script in PyMol that can do that?
>
> Best,
> Kanika
>
>
> --
> 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-d2dcopy2
> ___
> 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.
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[PyMOL] Rotation of a Protein

[kanika sharma]

Hello everyone,
I Have a protein with 2 chains.
I have to rotate the second chain of the protein by 60,120,180,240 degrees
each.
Is there a script in PyMol that can do that?

Best,
Kanika
--
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-d2dcopy2___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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