[Chimera-users] Unit cell

[Tom Goddard]

I still don’t understand. The atomic coordinates of one copy of the molecule is exactly what is in the PDB file.  The molecule extends beyond the unit cell box, but the whole molecule is the asymmetric unit so it would not make sense to truncate it to the atoms that lie within the box.  The unit cell box just shows visually the repeat pattern, the whole molecule has to be repeated with this brick spacing to see the crystal packing.

	Tom

> On Dec 1, 2016, at 12:19 PM, Neha Gandhi <n.gandhiau at gmail.com> wrote:
> 
> Yes the atomic coordinates within one unit cell.  
> 
> On 2 December 2016 at 06:10, Tom Goddard <goddard at sonic.net <mailto: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 <mailto: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 <mailto: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 <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <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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