[Chimera-users] Higher Order

Tom Goddard goddard at cgl.ucsf.edu
Sun Jan 11 16:26:09 PST 2009

Hi Hernando,

  The SMTRY and MTRIX records in PDB files are only used to describe 
crystal packing.  SMTRY describes only crystallographic symmetries.  
MTRIX describes only symmetries within the crystallographic asymmetric 
unit when the deposited coordinates do not contain the full crystal 
asymmetric unit (typically used for virus capsids).  Other cases, e.g. 
all electron microscopy structures use REMARK 350 biological unit BIOMT 
matrices.  See PDB 2tmv for an example of REMARK 350 for a helical 


hsosa at aecom.yu.edu wrote:
>     I have another related question: If I were to deposit a PDB 
> coordinates file of a helical structure,  what would be the best place 
> to put helical symmetry information (the file includes the  full 
> coordinates for only one asymmetric unit) so that chimera can generate a 
> model with more than one asymmetric unit ?. The idea  being to be able 
> to see the contacts between asymmetric units and  the symmetry of the 
> complex.   Should I use the the SMTRY,  or the  MTRIX  entries ?. Does 
> it make any difference in chimera ?.
> Thanks
> Hernando
> .

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