sculpt_complex_gui.py Command Help
Command: $SCHRODINGER/run sculpt_complex_gui.py
usage: sculpt_complex_gui.py -coord WHAT,WHAT,... -metal ATOMIC_SYMBOL
[-title STRUCTURE_TITLE] [-sqp] [-keep_h] [-h]
MAESTRO_FILE FILE_NAME
Sculpt one or more ligands around a metal atom Copyright Schrodinger, LLC. All
rights reserved.
positional arguments:
MAESTRO_FILE Structure file for the ligand that will be sculpted to
the central metal atom.
FILE_NAME Name of the output file to contain the sculpted
complex
options:
-coord WHAT,WHAT,... The specification of what binds to each coordination
site. The flag should be followed by a series of
comma-separated WHAT values, where each value is
either an integer or capping group name. There should
be one value per coordination site of the desired
VSEPR geometry, and the values must be listed in the
order shown in the coordination diagram of the Sculpt
Complex GUI for that geometry. An integer value of
WHAT refers to an atom number in the ligand structure
that binds to that site. A capping group name
indicates that the site is filled with a capping
group, and is taken from the following list: "none",
"hydrogen", "oxide", "hydroxyl", "fluoro", "chloro",
"bromo", "carbonyl", "methyl", "carboxyl", "amine",
"planar amine", "silyl", "thiol", "phosphyl". "none"
indicates that the coordinate site is to remain empty.
For example - a square pyramid geometry may be
specified for a tri-dentate ligand by using the six-
coordinate octahedral geoemtry and specifying the
coordination sites as follows: "-coord
7,10,methyl,15,methyl,none". This indicates that
ligand atoms 7, 10 and 15 occupy sites 1, 2 and 4,
while sites 3 and 5 are capped by methyl groups. Site
6 remains vacant, given the square pyramidal geometry.
(default: None)
-metal ATOMIC_SYMBOL Atomic symbol of the central atom of the complex.
(default: None)
-title STRUCTURE_TITLE
The title for the structure (default:
sculpted_complex)
-sqp For 4-coordinate complexes, the default geometry is
tetrahedral. Use this flag to use a square planar
geometry instead. (default: False)
-keep_h Keep hydrogen atoms attached to the ligand atoms that
coordinate to the metal. The default behavior is to
remove them. (default: False)
-h, -help Show this help message and exit.