Superimpose structures
[Menu-bar>Align] Two protein structures can be superimposed three-dimensionally using
C-alpha coordinates so that they are oriented in 3D-space in the same
way.
The mobile protein and the reference protein[s] are selected by the
user.
The user can specify a superposition method
.
Pressing 
finds an optimal rotation/translation that minimizes
the square root mean distance (RMSD) between C-alpha atoms of both proteins.
The result is displayed in a preview panel.
Only after pressing 
this transformation is applied to the mobile protein whereas the
target protein remains unchanged.
When the alignment is saved the transformation of the superimposed
protein will be written to HD.
These files are found int "./gaps/" and have the suffix ".3dTrans".
Residue subset Usually the entire protein structures
are used, but the calculation can also be confined to a subset of
residues such as "10-100,120-150".
Highlighting structurally equivalent residues:
Superposition can facilitate the alignment of proteins when the
3D-structures are similar while their sequence are not due to
divergent evolution (see 7373651). With the
Identify residues with certain structural features ... all residues adjacent
to the cursor position can be highlighted.
Writing PDB-files in new coordinates: See
Export protein in different format ....
Related sites: http://www.cgl.ucsf.edu/home/meng/grpmt/structalign-content.html