psico.msms

3. 2016 Thomas Holder, Schrodinger Inc.

License: BSD-2-Clause

Functions

atmtypenumbers([filename, selection, ...])	Update VDW radii for the given selection, based on "atmtypenumbers" file.
load_msms_surface(filename[, name, _colors, ...])	Load MSMS .vert and .face files as a CGO
msms_surface([selection, state, density, ...])	Run MSMS on the given selection and load the generated surface as a CGO.
save_xyzr(filename[, selection, state, ...])	Write the given selection to an xyzr or xyzrn (determined by extension) file for MSMS.

psico.msms.atmtypenumbers(filename='atmtypenumbers', selection='all', united=1, quiet=1, *, _self=...)

Update VDW radii for the given selection, based on “atmtypenumbers” file.

Arguments

filename = str: path to “atmtypenumbers” file

selection = str: atom selection to update {default: all}

united = 1: Use united (implicit hydrogens) radii {default} united = 0: Use explicit radii

Example

atmtypenumbers /tmp/MSMS-release/atmtypenumbers, united=0

psico.msms.load_msms_surface(filename, name='', _colors=None, *, _self=...)

Load MSMS .vert and .face files as a CGO

psico.msms.msms_surface(selection='polymer', state=1, density=3, name='', atomcolors=0, exe='msms', preserve=0, quiet=1, *, _self=...)

Run MSMS on the given selection and load the generated surface as a CGO.

Note that PyMOL’s own surface generation by default excludes atoms with the “ignore” flag. To match this behavior, use “polymer” (recommended) or “not flag 25” in your selection.

Arguments

selection = str: atom selection {default: polymer}

state = int: object state {default: 1}

density = float: MSMS surface point density {default: 3}

name = str: name of CGO object to create

atomcolors = 0/1: color surface by atom colors {default: 0}

Example

# optional: use Connolly radii atmtypenumbers /tmp/MSMS-release/atmtypenumbers

# show surface for protein msms_surface polymer

psico.msms.save_xyzr(filename, selection='all', state=1, _colorsout=None, *, _self=...)

Write the given selection to an xyzr or xyzrn (determined by extension) file for MSMS.