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Notes on recent commits (by file name):
======================================================================
plumed.py
======================================================================
This script now generates 2 files:
cmap (default name; change with --cmap filename)
plumed.dat (default name; no flag to change it)
----------------------------------------------------------------------
Make sure the inputs are in the GRO file format.
This is because the mapping of atoms to the
nearest non-symmetrical atom is defined within,
and the atoms used in the selection are based
on the GRO nomenclature.
Structure files can be converted to GRO format
using, for example, gmx editconf.
If you input two files with different atom
orders, a plumed.err file is created that shows
which atoms are out of order in the structures.
For the initial use of this plumed.dat file,
a custom version of plumed2 was used, available here:
https://github.com/bestlab/plumed2/tree/intermolecular-drmsd
======================================================================
plumed_residues.py
======================================================================
By default, this script now only generated the complete list of
residues that are in contact uniquely in each input (termed
'Inactive' and 'Active').
This file is named 'Unique_contact_residues.dat', and can be viewed
using any text parsing software (Nano, Vi, Libre/OpenOffice, etc.).
----------------------------------------------------------------------
The flags --gpcr, --pymol, and --vmd, do as follows:
--gpcr:
If the input protein is a GPCR, an input tab-separated value text
file with the complete list of Ballesteros-Weinstein numbers can be
given and the output is changed to reflect both residue numbers and
the corresponding Ballesteros-Weinstein numbers.
Example (from the rat Neurotensin receptor):
1x29 1.29 I61
1x30 1.30 Y62
1x31 1.31 S63
1x32 1.32 K64
1x33 1.33 V65
1x34 1.34 L66
1x35 1.35 V67
1x36 1.36 T68
1x37 1.37 A69
1x38 1.38 I70
1x39 1.39 Y71
1x40 1.40 L72
1x41 1.41 A73
1x42 1.42 L74
These numbers can be acquired from the GPCR database
(http://gpcrdb.org/), a very useful database for all information
GPCR related.
--pymol:
Additional to the base 'Unique_contact_residues.dat', the file
'PyMOL_representation.pml' is also created. To use it, open
PyMOL, load a PDB version of either input, and type:
@PyMOL_representation.pml
This will show all relevant residues as sticks, and remove
all hydrogens for the representation.
--vmd:
Same as above, only the file created, 'VMD_representation.tcl'
is used in VMD.
Load either input into VMD and, in the TKConsole, type:
source VMD_representation.tcl
It has the same effect as above.
The output file 'plumed_residues.err' is filled if there are atoms in
a different order (check above for more information).
======================================================================
readAndPlotCOLVAR.py
======================================================================
All plots generated using this script are saved as SVG (Scalable
Vector Graphics) files. This are larger than other image files,
and can be viewed using Inkscape (Unix), Eye of Gnome (Unix),
ImageMagick (Unix), and Gapplin (Mac), among others.
A data file can also be saved (in the csv format), using the
--save flag.
A working version of matplotlib is required to use this script.