Generate symmetry environment

[isohelio]

Hi,

Is there a gemmi command line option to generate the symmetry environment of a PDB file?

Or does this need to be done using the python API?

Many thanks
Mike

[wojdyr]

What do you mean? Whole unit cell or a biological unit?

[isohelio]

Hi, it was to generate a complete set of symmetry related asymmetric units that contact the initial structure. I have usually done this with my own software, but read elsewhere some discussion that this was more difficult than it appears for some structures. Or alternatively with all atoms within a specified distance.

I wondered if it was already an option for gemmi to produce this output.

Cheers,
Mike

[zhangfq-chemistry]

I encounter the same problem. It seems that point-group operations (rotational matrix) may help. Let me try.

[wojdyr]

Hi, it was to generate a complete set of symmetry related asymmetric units that contact the initial structure. I have usually done this with my own software, but read elsewhere some discussion that this was more difficult than it appears for some structures.

I added option --asus to gemmi contact to print all asymmetric units that are in contact. Example:

$ gemmi contact --asus 1keb.pdb 
x,y,z (+0,+1,+0)
x,y,z (-1,+0,+0)
x,y,z (+1,+0,-1)
x,y,z (+0,-1,+0)
x,y,z (+1,+0,+0)
x,y,z (+0,+0,-1)
x,y,z (+0,+0,+1)
$ gemmi contact --asus 3nwh.pdb
x,y,z (-1,+0,+0)
x,y,z (+5,+0,+1)
-x,y+1/2,-z (-6,+0,+0)
x,y,z (+1,+0,+0)

Or alternatively with all atoms within a specified distance.

If this is for visualization, that's something that crystallographic molecular viewers can do.
For example, Coot has option to show symmetry atoms in a specified radius.