[Chimera-users] Unit cell

[Neha Gandhi]

Yes the atomic coordinates within one unit cell.

On 2 December 2016 at 06:10, Tom Goddard <goddard at sonic.net> wrote:

> I don’t understand your question.  What do you mean by the “coordinates of
> the unit cell”?  Do you mean atom coordinates?  cell axis vectors?  How
> will you use this?
>
> Tom
>
> On Dec 1, 2016, at 11:56 AM, Neha Gandhi <n.gandhiau at gmail.com> wrote:
>
> Thank you Tom for your email.
>
> My apologies that my knowledge on microscopy structures is limited. I have
> a trivial question. Is there a way to extract the coordinates of the unit
> cell in Chimera rather than working with this 4 times long molecule? If I
> can do this then it will be easy to make copies or use contacts to get the
> neighboring molecules.
>
> Many thanks,
> Neha
>
> On 2 December 2016 at 05:04, Tom Goddard <goddard at sonic.net> wrote:
>
>> Hi Neha,
>>
>>   The space group for 3HR2 is P1 which means the unit cell contains only
>> one copy.  This is reported by the Chimera Unit Cell tool (menu Tools /
>> Higher-Order Structure / Unit Cell).  To show multiple copies press the
>> Options button on the Unit Cell dialog and change Number of Cells from 1 1
>> 1 to say 2 2 2 and press Make Copies to get molecule copies in a 2 by 2 by
>> 2 grid of unit cells.
>>
>>   It sounds like you also want the Unit Cell outline box to have corner
>> at (0,0,0) and that is not what happens.  Instead it shows another unit
>> cell outline that contains the center of the molecule.  This bizarre
>> structure is 4 times longer than the unit cell so the center likes in a
>> unit cell that does not have corner at (0,0,0).  Unfortnately the tool does
>> not let you show other unit cell outlines, just this one centered at the
>> molecule.  If you absolutely had to get a different unit cell outline you
>> could try to translate the outline model by multiples of the unit cell axes
>> vectors.  But you would need the coordinates of those vectors which would
>> be somewhat tricky to get since the cell is skewed.
>>
>> Tom
>>
>>
>>
>> On Nov 30, 2016, at 11:04 PM, Neha Gandhi wrote:
>>
>> Hi Elaine,
>>
>> I have tried to look at the unit cell information of pdb Id :3HR2. It is
>> a fiber diffraction structure of collagen with only CA coordinates. I tried
>> using different programs like VMD to visualise unit cell, the unit cell is
>> at the  beginning of N terminus in agreement with experimental paper.
>> Whereas in Chimera it is not the case. How can I visualize the unit cell of
>> 3HR2 structure in Chimera and also number of molecules within one unit cell?
>>
>> Many thanks,
>> Neha
>>
>> --
>> Regards,
>> Dr. Neha S. Gandhi,
>> Vice Chancellor's Research Fellow,
>> Queensland University of Technology,
>> 2 George Street, Brisbane, QLD 4000
>> Australia
>> LinkedIn
>> Research Gate
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>>
>
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/
> mailman/listinfo/chimera-users
>
>
>


-- 
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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