[Chimera-users] Unit cell
n.gandhiau at gmail.com
Thu Dec 1 12:19:42 PST 2016
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?
> 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,
> 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/mail
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Chimera-users