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<ccp4bb.l...@gmail.com> 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:
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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
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