This sounds as though you will create a 4-helical rod?
There are lots of 4-helical bundles but they arenot completely rod like
- there is a twist in most I have seen.
Maybe you should do secondary structure matching to a suitable 4-helicl
bundle, match your helix in turn to each of the bundle helices.
Eleanor
On 12/14/2011 02:13 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:
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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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