Thread: [PyMOL] Rotation of a Protein

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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

# 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 <ksh...@gm...> 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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

-- 
Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University

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 <http://maps.google.dk/>
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752

2011/10/7 kanika sharma <ksh...@gm...>

> 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 (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

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 <tl...@gm...>

> 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 <http://maps.google.dk/>
> 04107 Leipzig, Tyskland
> Mobil: +49 1577-8944752
>
>
>
> 2011/10/7 kanika sharma <ksh...@gm...>
>
>> 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 (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>

Create two new molecules from the originial.
then

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

2011/10/9 kanika sharma <ksh...@gm...>

> 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 <tl...@gm...>
>
>> 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 <http://maps.google.dk/>
>> 04107 Leipzig, Tyskland
>> Mobil: +49 1577-8944752
>>
>>
>>
>> 2011/10/7 kanika sharma <ksh...@gm...>
>>
>>>  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 (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>

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 <tl...@gm... 
> <mailto:tl...@gm...>>
> 
>     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 <http://maps.google.dk/>
>     04107 Leipzig, Tyskland
>     Mobil: +49 1577-8944752
> 
> 
> 
>     2011/10/7 kanika sharma <ksh...@gm...
>     <mailto:ksh...@gm...>>
> 
>         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

Thread: [PyMOL] Rotation of a Protein

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