Do you mean just any tetramer?
If so, Why not use an existing one - eg haemoglobin..
Eleanor
On 12/12/2011 09:42 PM, Fred wrote:
> I only want to produce an artificial tetramer.
>
>
>
> Em 12-12-2011 19:41, Jacob Keller escreveu:
>> Can you clarify your reason for doing this?
>>
>> JPK
>>
>> On Mon, Dec 12, 2011 at 3:36 PM, Fred<[log in to unmask]> wrote:
>>> Hi James,
>>> In my first post "arbitrary orientation into the cell" only means not
>>> parallel to any crystallographic axis, which would simplify things very
>>> much. I want to apply the 4-fold axis to the protein coordinates. If
>>> I have
>>> a cell and therefore an origin, I can take a point at any distance of
>>> the
>>> origin, pass a vector/axis through it and take the 3 others molecules by
>>> symmetry. That's trivial, given the point, the orientation and the
>>> property
>>> of the rotation. Don't know which program to use.
>>> Regards,
>>> Fred
>>>
>>>
>>>
>>> Em 12-12-2011 19:18, James Stroud escreveu:
>>>
>>>> This is not trivial. Assuming an arbitrary origin, the simplest 4-fold
>>>> symmetry operation (4-fold rotation) has 5 free parameters (translation
>>>> along the symmetry axis is irrelevant). The biggest problem is
>>>> determining
>>>> the values for these parameters. For example, once you apply the
>>>> symmetry,
>>>> your molecule may clash with its symmetry mates or not even contact
>>>> them.
>>>> And even if you solve this latter problem automatically (which is not
>>>> trivial because of irregularity), that leaves a net of 3 parameters
>>>> describing the orientation of the protomer.
>>>>
>>>> James
>>>>
>>>>
>>>>
>>>> On Dec 12, 2011, at 1:34 PM, Fred wrote:
>>>>
>>>>> Hi Tim,
>>>>> Thanks for your message and sorry if I wasn't clear. I don't have
>>>>> neither
>>>>> the axis orientation nor the rotation matrix. I would like to
>>>>> create them
>>>>> but don't know how and which program to use. Theoretically a have
>>>>> to create
>>>>> a axis (vector) at some distance of the molecule into the cell and
>>>>> give it
>>>>> the 4-fold propriety. Quite simple, but don't which program to use.
>>>>> Regards,
>>>>> Fred
>>>>>
>>>>>
>>>>> Em 12-12-2011 18:23, Tim Gruene escreveu:
>>>>>> -----BEGIN PGP SIGNED MESSAGE-----
>>>>>> Hash: SHA1
>>>>>>
>>>>>> Hello Fred,
>>>>>>
>>>>>> if you know the rotation matrix, you can use pdbset with its 'rotate'
>>>>>> keyword.
>>>>>> It is not clear to me whether or not you have the rotation matrix
>>>>>> or how
>>>>>> you define rotation.
>>>>>>
>>>>>> Cheers,
>>>>>> Tim
>>>>>>
>>>>>> On 12/12/2011 08:49 PM, Fred wrote:
>>>>>>> Hi List,
>>>>>>> I would like to build an artificial tetramer from a monomer PBD
>>>>>>> file.
>>>>>>> All that I have is the coordinates it self with CRYST/CELL
>>>>>>> information
>>>>>>> cards. The artificial 4-fold axis has an arbitrary orientation
>>>>>>> into the
>>>>>>> cell. I mean, its not parallel to any crystallographic axis and
>>>>>>> have to
>>>>>>> be at a certain distance of the molecule. This sounds conceptually
>>>>>>> simple, but I would like to do that in batch mode for hundreds of
>>>>>>> PDB's.
>>>>>>> Could someone, please, tell me the easiest way/program to do that?
>>>>>>> Thanks in advance,
>>>>>>> Fred
>>>>>>>
>>>>>> - -- - --
>>>>>> Dr Tim Gruene
>>>>>> Institut fuer anorganische Chemie
>>>>>> Tammannstr. 4
>>>>>> D-37077 Goettingen
>>>>>>
>>>>>> GPG Key ID = A46BEE1A
>>>>>>
>>>>>> -----BEGIN PGP SIGNATURE-----
>>>>>> Version: GnuPG v1.4.10 (GNU/Linux)
>>>>>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>>>>>
>>>>>> iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn
>>>>>> cqs8GHOu5M3JQahA/CofR1k=
>>>>>> =tDUj
>>>>>> -----END PGP SIGNATURE-----
>>
>>
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