[phenixbb] Non crystallographic symmetry

Pavel Afonine pafonine at lbl.gov
Thu Oct 1 17:43:06 PDT 2015

Hi Reza,

you can have as many as you can fit into memory of your computer.

Note, you need to provide the whole molecule as the input (not one copy 
plus MTRIX/BIOMT matrices). If you only have one copy plus MTRIX/BIOMT 
matrices you can use phenix.pdb.mtrix_reconstruction or 
phenix.pdb.biomt_reconstruction tools to obtain the whole model (the GUI 
equivalents of these command line tools are available, I think).

Running real-space refinement (phenix.real_space_refine) would be less 
memory intensive than reciprocal space refinement (phenix.refine). You 
did not mention what data you have, X-ray or Cryo-EM, so I would not 
tell much about this.

Anyway, you should be able to do what you want without problems. If you 
have any questions or problems or need any help please let me know!

Good luck!

On 10/1/15 17:10, Reza Khayat wrote:
> Hi,
> I need to use icosahedral symmetry to refine a virus crystal 
> structure. Does phenix support 60 NCS matrices? If not, how should I 
> go about recompiling the program so that I can have 60 NCS matrices?
> Best wishes,
> Reza
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
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