[Chimera-users] Unit cell
n.gandhiau at gmail.com
Thu Dec 1 11:56:58 PST 2016
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
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.
> 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,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Research Gate
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
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