-
Notifications
You must be signed in to change notification settings - Fork 1
/
README
152 lines (106 loc) · 6.3 KB
/
README
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
If you want to gain the people's ovation and fame forever, document your stuff here!
List the files you've added and way briefly what kind of stuff is in them and their
status (mostly, if they're for public consumption or not). I'll start:
PackingMeasureUtils.py
contains stuff for viewing "*_packing.pdb" files. Should mostly work,
so use these without fear (be careful what you use as radii though...).
loadPackingPDB <file> , [<name for object>]
loads a foo_packing.pdb file and colors it all pretty-like
creates two selections along with the loaded object called
NAMEcavities and NAMEprotein which are the heteratoms representing
holes and everything else, respectively. Names can get pretty long,
by pymol lets you do good stuff like "select NA*cav*", which will
match a selection called NAMEISREALLYLONGcavities.
expandRadii byamount, selection
contractRadii byamount, selection
These do just what they say. A rebuild is triggered, so they're not instantaneous
useOccRadii selection
useTempRadii selection
will take VDW radii from PDB occ/bfac cols and use them as radii
useTempColors selection
useOccColors selection
Colors by occ/bfac from pdb
useRosettaRadii
changes standard radii to match rosetta
PDBBrowser.py
contains some quick and dirty functions for browsing a bunch of PDBs
Experimental! My not work right for you.
loadFromGlob pattern, name=None, native=None, delete=True, pickrandom=F
This takes a shell style pattern like ~/mypdbs/foobar_*_packing.pdb and
loads one of the files. If the file ends with _packing.pdb[.gz] it uses
loadPackingPdb. If pattern is just a directory, it'll browse the .pdb/.pdb.gz
files in that dir
pickrand = True, it'll pick a random one.
name = optional name for loaded objcet
native arg provides a native for reference, although I don't think
does anything as yet.
loadPrev / loadNext
go back and fourth in the structures you've browsed. this will actually
load and delete them, so they don't have to stay in pymol. uses the globals
LOADLIST and POINTER.
browseReset
resets browsing history (LOADLIST and POINTER)
rosetta_tools.py
This is a PyMOL plugin which can be used to highlight certain features on proteins.
Currently there are two functions implemented:
Hydrogen bond visualization
This function displays hydrogen bonds to help with evaluating de novo designed
structures and designed interfaces. The bonds are created as CGO objects (native
to PyMOL) and are colored in gradient from yellow (for good, low-energy hydrogen
bonds) to white (weak H-bonds).
Surface hydrophobic patch visualization
This function of the plugin identifies hydrophobic patches on the surface of
all visible objects and colors them.
The plugin requires the following things:
- python, version >= 2.4
Note: If you have old versions of python on your machine, make sure PyMOL uses version
2.4 or greater. The plugin will NOT work for python v2.3. It may be necessary to
reinstall PyMOL or completely remove older version of python to get this to work.
- The X11 version of PyMOL
MAC users: Only the X11 version of PyMOL is capable of running plugins. You will
need to obtain the PyMOLX11Hybrid version of PyMOL from the PyMOL Web site if
you are running MacPyMOL.
Hydrogen bond visualization only:
- A compiled copy of Rosetta and the Rosetta database somewhere on your machine.
Hydrophobic patch visualization only:
- A compiled copy of the QUILT patch identification algorithm (available for download
from ftp://ftp.ebi.ac.uk/pub/contrib/lijnzaad/)
To install the plugin, follow these instructions:
1) Locate the PyMOL plugins folder and create a symbolic link to the file 'rosetta_tools.py'
in this folder. The commands for this will look something like below:
cd /path/to/pymol/modules/pmg_tk/startup
ln -s /path/to/rosetta_tools.py rosetta_tools.py
For hydrogen bond visualization:
2a) Locate the src/pilot_apps.src.settings.all file in your Rosetta directory and add in
compilation of the executable 'report_hbonds_for_plugin' by adding the following lines:
"pilot/ronj" : [
"report_hbonds_for_plugin",
],
Then compile it:
scons mode=release bin/report_hbonds_for_plugin.{linux|macos}gccrelease
3) In your HOME directory (check your environment by typing 'env'), create a file named
".rosettatoolsplugin" and put the following two lines in it:
rosetta_executable /path/to/mini/bin/report_hbonds_for_plugin.linuxgccrelease
rosetta_database /path/to/minirosetta_database/
This file is necessary so that the PyMOL plugin knows how to find Rosetta and the database.
4) Run PyMOL
5) With a structure loaded, click on "Plugins -> Rosetta Tools -> display hydrogen bonds".
Note: PyMOL must be started from the same directory as the loaded PDB file so that the plugin
can find it. Hydrogen bonds across chains only can be drawn using the menu item
"Plugins -> Rosetta Tools -> display hydrogen bonds, interface only"
The bonds are colored by a gradient:
Yellow ====> good score
White ====> bad score
Energies are displayed for bonds across chains.
For hydrophobic patch visualization:
2a) Compile QUILT according to the instruction provided in the README.
3) In your HOME directory, create or append to a file named ".rosettatoolsplugin" the following
line in it:
quilt_executable /path/to/quilt/src/quilt
4) Copy the files 'ATOMS' and 'RESIDUES' distributed with the quilt src to your HOME directory.
cp /path/to/quilt/ATOMS ~/.atoms
cp /path/to/quilt/RESIDUES ~/.residues
5) Run PyMOL
6) With a structure loaded, click on "Plugins -> Rosetta Tools -> display hydrophobic patches".
The plugin will change the protein to spherical represenation and will color the three largest
hydrophobic patches dark green (largest), palegreen, and gray (3rd largest).