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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