An old old trick for getting a straight helix along a crystal axis using
the GUI.
Run the Amore TABLING step - it is part of the GUI with the helix as
your "model". (See molecular replacement - amore suite.)
Amore calculates the ppl axes and will align it along the Z axis ..
Thank you Jorge..
Eleanor
On 12/14/2011 03:07 PM, Tim Gruene wrote:
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Hello Fred,
as far as I understand your problem I am not aware of existing programs
to carry out the tasks. To automatise the process I would write a
program myself which takes the PDB-file and the reside numbers which
make that helix as input and:
1) determine the axis of that straight helix (probably by determining
the moments of intertia, see e.g. Gruene, T.& Sheldrick, G. M. (2011).
Acta Cryst. A67, 1-8, section 2.2.1 with x_o the centre of mass.
2) copy the monomer by 3 rotations of 90 degrees about this axis to get
the tetramer.
3) move each of the four monomers stepwise perpendicularly to the
rotation axis until no more clashes are there (mask the volume of one
monomer and check each atom/atom volume whether it falls into that
volume. Because of the 4-fold rotation axis you only need to mask one
monomer and check against its next and its opposite neighbour).
The tricky bit w.r.t automatisation would be to determine the helix
axis, unless you already have a list of composing residues for each
PDB-file.
That's probably nothing I would finish in a week's time, though...
Tim
On 12/14/2011 03:13 PM, Fred wrote:
Hi Tim,
Thanks for your replay. All pdb monomers have the same primary sequence
and a perfect matching long helix, which I have used to superpose the
coordinates. Such helix is almost straight so that, the idea would be to
create a vector along the helix main axis, shift this axis to a some
distance (perhaps minimizing clashes) and apply 4-fold rotation. A
second step would be to take these into pdbset to make things in batch
mode. It sounds simple, but don't know the easiest way/programs to do
that. I can do just the basics in Coot. I remember that Xfit had some
options to trace vectors inside a cell and give it rotation properties.
However, Xfit seems to be frozen and integration with pdbset would be
painful.
Regards,
Fred
Em 14-12-2011 07:32, Tim Gruene escreveu:
Hi Fred,
this sentence of yours, "All pdb's are superposed by a common sequence
region, which also will be part of the tetramer interface." probably
hides the information which would be necessary for a reasonable answer
to your question.
If you still are stuck, you might post again with a more detailed
description of what you mean.
Cheers, Tim
On 12/13/2011 07:28 PM, Fred wrote:
Dear CCP4bb list,
Thank you very much all of you who have answered my post. I'm really
sorry if I was unclear. Such operation is so unusual that I could be
able to express myself appropriately. From quick reading some replies
(James Stroud and Guillaume Ponchel), it seems is possible do build
artificial tetramers with Coot. Several problems have been raised like
clashes, unusual interfaces and so on. A second step would be to take
Coot's rotation and translation matrix and apply it to all pdb's in
batch mode with pdbset. All pdb's are superposed by a common sequence
region, which also will be part of the tetramer interface. I'll try to
make things work.
Once more, sorry for any inconvenience and thank you very much.
Kind regards,
Fred
-- - --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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