[Chimera-users] conjoined unit cells

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 19 10:51:35 PDT 2007

Hi Bartek,
Although the Unit Cell tool generates only a single unit cell, the  
Multiscale Models tool can generate a 3x3x3 block of unit cells.   It  
is under Tools... Higher-Order Structure.  Choose the Multimer option  
"3x3x3 crystal unit cells" and then click "Make models".

See the man page for more details on Multiscale Models:

A possibly tricky thing is that for computational expediency,  
Multiscale Models first generates only low-resolution surfaces for  
all the additional copies.  If you need atomic coordinates for some  
or all of those copies, select those copies in Multiscale Models and  
then choose a different Style of display.  All the styles other than  
Surface force loading of the atomic coordinates (Ribbon, Wire, Stick,  
Ball&Stick, Sphere).  Loading coordinates for the copies creates  
additional molecule models in Chimera.  Their coordinates can be  
saved to file(s) with File... Save PDB in the main Chimera menu.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 19, 2007, at 7:22 AM, Bartosz Siemiński wrote:

> Hi all,
> I was working with Chimera for some time, beeing
> convinced  I don't need no help, until I'd got to
> this.
> Is there a possibility of conjoining several (let's
> say four, nine or sixteen) unit cells? I use the el.
> density map (converted to cpp4, so it could be loaded
> by Chimera) for structural alignment and such an
> operation would be very usefull.
> Thanks in advance,
> Bartek

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