Euclidian Model Matching

phenix.emma

EMMA stands for Euclidean Model Matching and is the algorithm used by HySS to superimpose two putative solutions and to derive the consensus model. The same algorithm is also available through the external phenix.emma command-line interface. Enter phenix.emma without arguments to obtain the help page:

usage: phenix.emma [options] reference_coordinates reference_coordinates other_coordinates

options:
  -h, --help            show this help message and exit
  --unit_cell=10,10,20,90,90,120|FILENAME
                        External unit cell parameters
  --space_group=P212121|FILENAME
                        External space group symbol
  --symmetry=FILENAME   External file with symmetry information
  --tolerance=FLOAT     match tolerance
  --diffraction_index_equivalent
                        Use only if models are diffraction-index equivalent.

Example: phenix.emma model1.pdb model2.sdb

The command takes two coordinate files in various formats (.pdb, CNS .sdb, SOLVE output, SHELX .ins) and compares the structures taking the space group symmetry, the allowed origin shifts and the hand ambiguity into account. The output is similar to the Match summary shown above in the example HySS output.

The match tolerance defaults to 3 Angstrom. For structures obtained with very low resolution data it may be necessary to specify a different tolerance, e.g. --tolerance=5.

The --symmetry option works just like it does for phenix.hyss. It can be used to extract symmetry information from external files such as input files for other programs (CNS, SHELX, SOLVE, ...) or reflection files. However, the --symmetry option is only required if the information about the unit cell and the space group is missing in both coordinate files given to phenix.emma.

phenix.emma conducts an exhaustive search and, in contrast to HySS, displays all possible matches. The match with the largest number of matching sites is shown first, the match with the smallest number of matching sites is shown last (often just one site). Therefore you have to look at the beginning of the output to see the best match. I.e. if the output goes to the screen don't let yourself get distracted if you see a large number of Singles near the end of the output. Scroll back to see the best match.

Emma is also available via a web interface.