[Chimera-users] Unit cell

[Neha Gandhi]

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
> _______________________________________________
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20161202/c1c9b8f7/attachment.html>