diff options
Diffstat (limited to 'doc/man/cell_tool.1')
| -rw-r--r-- | doc/man/cell_tool.1 | 12 |
1 files changed, 6 insertions, 6 deletions
diff --git a/doc/man/cell_tool.1 b/doc/man/cell_tool.1 index 08f22d68..d5ce57af 100644 --- a/doc/man/cell_tool.1 +++ b/doc/man/cell_tool.1 @@ -76,11 +76,11 @@ $ cell_tool --find-ambi 1JB0.pdb -y 6 .nf [...] Observed symmetry operations: - 1 : hkl -h-k,k,-l -h-k,h,l -h,-k,l -h,h+k,-l + Observed : hkl -h-k,k,-l -h-k,h,l -h,-k,l -h,h+k,-l -k,-h,-l -k,h+k,l k,-h-k,l k,h,-l h,-h-k,-l h+k,-h,l h+k,-k,-l Ambiguity operations: - 1 -> 6 : hkl -h-k,k,-l + Observed -> 6 : -h-k,k,-l .fi There are 12 reflections which cannot be distinguished between by the lattice alone, but only 6 of those are true symmetry equivalents according to the structure. The transformation describing the indexing ambiguity as follows: "A reflection hkl will be confused with one with indices -h-k,k,-l". Had the point group of the crystals been '622', there would have been no indexing ambiguity (try it!). @@ -97,10 +97,10 @@ Observed symmetry operations: 1 : hkl -h,-k,l -h,k,-l -k,-h,-l -k,h,l k,-h,l k,h,-l h,-k,-l Ambiguity operations: - 1 -> 422 : hkl +Observed -> 422 : .fi -All of the apparently equivalent reflections are true symmetry equivalents according to point group 422, so there is no indexing ambiguity. The only operation produced by left coset decomposition is the identity operation. +All of the apparently equivalent reflections are true symmetry equivalents according to point group 422, so there is no indexing ambiguity. No operations are produced by the left coset decomposition. .PP \fBExample 3: "Accidental" ambiguity in myoglobin\fR @@ -117,9 +117,9 @@ $ cell_tool --find-ambi 3VAU.pdb -y 2_uab 3.51 2.84 6.33 nm 90.00 106.84 90.00 deg [...] Observed symmetry operations: - 1 : hkl -h,-k,h+l -h,k,-l h,-k,-h-l + Observed : hkl -h,-k,h+l -h,k,-l h,-k,-h-l Ambiguity operations: - 1 -> 2 : hkl -h,-k,h+l + Observed -> 2 : -h,-k,h+l .fi The transformations '-h,-k,h+l' and 'h,-k,-h-l', which correspond to indexing "diagonally", produce cells which look very similar to the original cell - a difference of only 0.4A and 1.34 degrees. These two transformations are themselves related by a twofold rotation, which is a true symmetry of this crystal structure. There is therefore only one ambiguity transformation. The transformation is strange because it isn't one of the symmetries displayed by a monoclinic lattice in general. This ambiguity has arisen because of of the particular unit cell parameters for this structure. |