[Chimera-users] on chimera unit cell function

Elaine Meng meng at cgl.ucsf.edu
Sun Jan 29 12:05:22 PST 2017


Hi Smith,
The number of copies and their positions are all correct no matter whether you choose the “pack” option or not.  If you cut out a part of the real crystal, there will be a real copy in the same place as the copy from Chimera.  So imagine if you had specified an infinite (or large) number of unit cells in Chimera, a chunk from the middle of the result would look the same as some chunk of the real idealized crystal, regardless of whether you used “pack”.  However, since you are probably specifying 1 x 1 x 1 or some small number of unit cells, yes choose the “pack” option to show the copies packed together, instead of with some spaces where a copy is shown inside a neighboring box rather than in the central outline box.
Best,
Elaine

> On Jan 29, 2017, at 5:10 AM, Smith Liu <smith_liu123 at 163.com> wrote:
> 
> Dear Elaine,
> 
> I am still confusing on the function of "Pack molecules in unit cell" in Chimera. If we cut out a cube (or a volume) of crystal based on which a pdb was got, do you think the molecules packed in the cube in the way without "Pack molecules in unit cell" clicked, or the molecules packed in the cube in the way with "Pack molecules in unit cell" clicked?
> 
> I am looking forward to getting a reply from you.
> 
> Smith
> 
> 
> At 2017-01-29 00:50:44, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
> >Hi Smith,
> >It is my understanding that you will get the same number of copies whether or not you choose the “pack” option, and that there are multiple equally correct ways in which the copies will be positioned according to the symmetry information.  The “pack” option simply chooses, out of these many equally correct alternatives, a configuration that places the centers of all the copies inside one unit cell outline box instead of spreading them out among neighboring boxes.
> >I hope this helps,
> >Elaine
> >-----
> >Elaine C. Meng, Ph.D.                       
> >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> >Department of Pharmaceutical Chemistry
> >University of California, San Francisco
> > 
> >> On Jan 28, 2017, at 1:47 AM, Smith Liu <smith_liu123 at 163.com> wrote:
> >> 
> >> Dear All,
> >> 
> >> In Chimera, we do Tools →Higher-Order Structure→Unit Cell, then what will be the diffenrence if we clicked "Pack molecules in unit cell" in comparison with if we did not click "Pack molecules in unit cell"? Does it mean that what we observed (or what Chimera displayed) if we click "Pack molecules in unit cell" , was really part of what it displayed if we did not click "Pack molecules in unit cell" but we increased the "Number of Cells" significantly?
> >> 
> >> I am looking forward to getting a reply from you.
> >> 
> >> Smith




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