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:
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> 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
>
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