Metal Geometry 
Metal Geometry is a tool for analyzing metal ion
coordination geometries. It also allows adding or deleting coordination
pseudobonds.
See also:
Structure Measurements,
FindHBond,
Build Structure,
PseudoBond Reader
There are several ways to start
Metal Geometry, a tool in the Structure Analysis category.
If more than one metal ion is present, the ion of interest should be chosen
from the pulldown menu at the top of the dialog.
Metal Geometry can also be started by
by double-picking
a metal ion from the graphics window (doubleclicking it with the button
assigned to picking)
and choosing Coordination Geometry from the resulting context menu.
The view in the graphics window
will focus on the specified metal ion and nearby atoms.
The Metal transparency slider allows adjusting the transparency of the
displayed metal ion.
The Coordination Table lists atoms that might
be coordinated to the metal ion, sorted by distance.
Each row represents a ligation set comprised of not only the atom
named in that row, but also all of the atoms in the rows above it.
Clicking a row chooses that ligation set as the
current ligation set and
selects its atoms.
The rows cannot be reordered, but atoms can be added to or removed from the
list by selecting them in
the graphics window and clicking the
Add or Remove buttons on the right. Columns:
- Coordinator - a potentially metal-ligating atom, listed in the
Atomspec display style specified in the
General preferences
- Distance (Å)
- distance in Å from that atom to the metal ion
- Angle RMSD
- root-mean-square deviation (RMSD) of the angles in the
ligation set
from those in the idealized Best Geometry for that set
- Best Geometry - the coordination geometry for which the
ligation set has the lowest Angle RMSD
(additional geometries can be shown in the
Geometry Table)
Clicking Create/Update will generate or delete coordination
pseudobonds to the
metal as needed to represent the current ligation set.
Clicking Display options... brings up a list of
pseudobond attributes
for this group, allowing changes in properties
such as color, linewidth, and whether the lines are dashed.
When an individual
pseudobond
is selected,
its attributes
can be altered with the
Selection Inspector.
The Geometry Table
lists possible metal coordination geometries
for the current ligation set,
subject to certain screens.
Columns:
- Geometry - coordination geometry
- Coord. Number
- total number of metal-ligating atoms needed to fill
the Geometry
- Angle RMSD - RMSD of the angles
for the current ligation set
from those in the idealized Geometry
(the Geometry for which this is lowest is reported as the
Best Geometry in the
Coordination Table)
Clicking a row in the Geometry Table chooses that
metal coordination geometry. Depict idealized geometry
shows the chosen geometry with arrow objects,
and water oxygens can be Added to occupy any unfilled sites.
The distance from the metal at which to add water oxygens
is automatically set to the average for the
current ligation set, but can be edited.
Unlikely geometries can be screened out of the tables:
- Screen unfilled geometries (default off)
- disregard coordination geometries with
coordination number greater than the
number of atoms in the current ligation set
- Screen "overcrowded" geometries (default on)
- disregard coordination geometries that would place ligating atoms too close
together, given their likely distance from the metal ion.
Clicking Show parameters expands the dialog to reveal additional
settings for this screen:
A geometry is considered overcrowded if hypothetical metal-ligating atoms
placed at the ideal angles for that geometry, at a distance equal to the
[average | maximum | minimum ] of the actual chosen ligating atoms,
would be less than mindist (default 2.8) Å apart.
Clicking Hide parameters hides the overcrowding settings.
Close closes the Metal Geometry dialog.
Help opens this manual page in a browser window.
UCSF Computer Graphics Laboratory / July 2010