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startupAliases.py
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startupAliases.py
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from __future__ import print_function
# -*- coding: utf-8 -*-
"""
DESCRIPTION
On the startup of PyMOL, this script defines a number of aliases.
The aliases are listed here instead of in the pymolrc file
to avoid clutter of the command history window. Source this
file from your .pymolrc file on the mac or linux or
from your pymolrc.pml file on Windows by adding the command:
run ~/Scripts/PyMOLScripts/startupAliases.py
Requires quat.py from the PyMOL Wiki
(http://www.pymolwiki.org/index.php/BiologicalUnit/Quat)
Store quat.py in ~/Scripts/PyMOLScripts/.
Tested on PyMOL versions 1.5.0.5, 1.8.0.5, 1.8.1.0 and 1.8.2.0
No guarantee is given that this script will work with older
or newer versions of PyMOL.
Copyright Notice
================
Copyright (C) 2016 Blaine Mooers
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details:
http://www.gnu.org/licenses/.
The source code in this file is copyrighted, but you can
freely use and copy it as long as you don't change or remove any of
the copyright notices.
Blaine Mooers , PhD
blaine-mooers@ouhsc.edu
975 NE 10th St, BRC 466
University of Oklahoma Health Sciences Center,
Oklahoma City, OK, USA 73104
"""
from pymol import cmd
__author__ = "Blaine Mooers"
__copyright__ = "Blaine Mooers, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA 73104"
__license__ = "GPL-3"
__version__ = "1.0.3"
__credits__ = ["William Beasley","Chiedza Kanyumbu"]
# people who reported bug fixes, made suggestions, etc.
__date__ = "24 July 2016"
__maintainer__ = "Blaine Mooers"
__email__ = "blaine-mooers@ouhsc.edu"
__status__ = "Production"
def SA():
'''
DESCRIPTION
startupAliases.py Copyright (C) 2016 Blaine Mooers.
This script comes with ABSOLUTELY NO WARRANTY; for details,
please see the license file.
Copy to ~/Scripts/PyMOLScripts/.
Add this command on one line in your .pymolrc file
(pymolrc.pml on Windows):
run ~/Scripts/PyMOLScripts/startupAliases.py
Format of list below:
alias name, description of alias: PDB code (where applicable).
Molecules in standard orientations:
T4L, WT T4 lysozyme (1.09 ang) as a ribbon diagram: 3fa0.
U8, 16-mer dsRNA with 8 contiguous Us. U-helix RaNA (1.37 ang): 3nd3.
WC8, 16-mer RNA with all Watson-Crick base pairs (1.52 ang): 3nd4.
N9, neuraminidase as cartoon, biological unit (1.55 ang): 4dgr.
GGT, gamma glutamyl transpeptidase as cartoon (1.67 ang): 4gdx.
GU, 10-mer RNA with eight GU base pairs (1.32 ang): 4pco.
Complex figures to serve as templates:
BST, Base-stacking figure, (1.32 ang): 4pco.
LG, Electron density map of nine sugar glycan (1.55 ang): 4dgr.
NA, Sodium cation in major groove of 16-mer RNA (1.52 ang): 3nd4.
Complex representations applied to any visible molecular object:
AO, Make ambient occlusion image. Requires global view of protein.
BU, Display biological unit.
CB, Define color blind compatible coloring scheme.
BW, Make black and white ribbon cartoon on white background.
CSS, Color ribbon and cartoons by secondary structure: red, green and yellow.
CBSS, Color ribbon and cartoons with colorblind friendly colors.
CR, Make colored filled-ring cartoon of nucleic acids..
FR, Make filled-ring cartoon of nucleic acids.
SE, Make SAXS envelope from a bead model.
Type the alias name to execute the commands. The names are case sensitive.
Type 'help <AliasName>' (e.g., help T4L) for a description of the
alias and for two sets of commands. The first set of commands has
line breaks for easy selection single lines of commands. The second
set of commands is one one line for easy copying and pasting of the
entire horizontal script. The commands can be copied from the
command history window and pasted onto the command line for code
reuse. Some aliases require additional scripts.
Type 'SA' to refresh the list of aliases.
Type 'help rline' to see commands for moving cursor on the command line.
'''
print(SA.__doc__)
cmd.extend('SA',SA)
def T4L():
'''
DESCRIPTION
WT T4 lysozyme as ribbon diagram (1.08 Ang): 3FA0.
USAGE
Type 'T4L' to activate. Type 'help T4L' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
delete all;
fetch 3fa0,type=pdb,async=0;
orient;
turn z,-90;
turn y,-5;
turn x,10;
hide everything;
bg_color white;
show cartoon;
color red, ss H;
color yellow, ss S;
color green, ss L+;
set_view (-0.18,-0.69,-0.7,0.98,-0.17,-0.09,-0.06,-0.7,0.71,0.0,0.0,-165.67,34.77,11.27,9.52,132.07,199.27,-20.0);
ray 1500,1600;
The commands without linebreaks:
delete all;fetch 3fa0,type=pdb,async=0;orient;turn z,-90;turn y,-5;turn x,10; hide everything; bg_color white;show cartoon;color red, ss H;color yellow, ss S;color green, ss L+;set_view (-0.18,-0.69,-0.7,0.98,-0.17,-0.09,-0.06,-0.7,0.71,0.0,0.0,-165.67,34.77,11.27,9.52,132.07,199.27,-20.0); ray 1500,1600;
'''
cmd.reinitialize()
cmd.fetch('3fa0', type='pdb', async='0')
cmd.orient()
cmd.turn('z', '-90')
cmd.turn('y', '-5')
cmd.turn('x', '10')
cmd.hide('everything')
cmd.bg_color('white')
cmd.show('cartoon')
cmd.color('red', 'ss H')
cmd.color('yellow', 'ss S')
cmd.color('green', 'ss L+')
cmd.set_view('(-0.18,-0.69,-0.7,0.98,-0.17,-0.09,-0.06,-0.7,0.71,0.0,0.0,-165.67,34.77,11.27,9.52,132.07,199.27,-20.0)')
cmd.ray('1500', '1600')
cmd.extend('T4L',T4L)
def U8():
'''
DESCRIPTION
16-mer dsRNA with 8 contiguous Us. U-helix RNA (1.37 Ang): 3nd3.
Has one strand in the asymmetric unit. Uses quat.py to generate
the second strand. Cartoon with filled rings and bases cartoon.
USAGE
Type 'U8' to activate. Type 'help U8' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
delete all;
fetch 3nd3,type=pdb,async=0;
run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py;
quat 3nd3;
hide everything;
bg_color white;
show sticks;
set cartoon_ring_mode, 3;
set cartoon_ring_finder, 1;
set cartoon_ladder_mode, 1;
set cartoon_nucleic_acid_mode, 4;
set cartoon_ring_transparency, 0.5;
as cartoon;
set_view (-1.0,-0.03,0.06,-0.06,0.01,-1.0,0.04,-1.0,-0.01,-0.09,-0.02,-168.02,7.85,15.56,-0.21,137.38,199.33,-20.0);draw;
The commands without linebreaks:
delete all;fetch 3nd3,type=pdb,async=0;run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py;quat 3nd3;hide everything;bg_color white; show sticks;set cartoon_ring_mode, 3;set cartoon_ring_finder, 1;set cartoon_ladder_mode, 1;set cartoon_nucleic_acid_mode, 4;set cartoon_ring_transparency, 0.5;as cartoon;set_view (-1.0,-0.03,0.06,-0.06,0.01,-1.0,0.04,-1.0,-0.01,-0.09,-0.02,-168.02,7.85,15.56,-0.21,137.38,199.33,-20.0);draw;
'''
cmd.reinitialize()
cmd.fetch('3nd3', type='pdb', async='0')
cmd.do('run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py')
cmd.do('quat 3nd3')
cmd.hide('everything')
cmd.bg_color('white')
cmd.show('sticks')
cmd.set('cartoon_ring_mode', '3')
cmd.set('cartoon_ring_finder', '1')
cmd.set('cartoon_ladder_mode', '1')
cmd.set('cartoon_nucleic_acid_mode', '4')
cmd.set('cartoon_ring_transparency', '0.5')
cmd.show_as('cartoon')
cmd.set_view('(-1.0,-0.03,0.06,-0.06,0.01,-1.0,0.04,-1.0,-0.01,-0.09,-0.02,-168.02,7.85,15.56,-0.21,137.38,199.33,-20.0)')
cmd.draw()
cmd.extend('U8',U8)
def WC8():
'''
DESCRIPTION
16-mer dsRNA, Watson-Crick helix RNA. 1.55 Angstrom
resolution: 3nd4. Has one strand in the asymmetric unit.
Needs quat.py to generate the second strand. Use the
BU alias. Cartoon with filled rings and bases cartoon.
USAGE
Type 'WC8' to activate. Type 'help WC8' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
delete all;
fetch 3nd4,type=pdb,async=0;
hide everything;
run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py;
quat 3nd4;
bg_color white;
show sticks;
set stick_radius, 0.12;
set nb_spheres_size, 0.25;
show nb_spheres;
set stick_ball, on;
set stick_ball_ratio, 1.8;
set_view (-0.99,-0.03,0.17,-0.18,0.02,-0.98,0.03,-1.0,-0.03,0.0,0.0,-169.97,8.1,15.62,-1.69,139.24,200.7,-20.0);
hide everything,name H*;
rock
The commands without linebreaks:
delete all; fetch 3nd4,type=pdb,async=0;hide everything; run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py; quat 3nd4;bg_color white; show sticks; set stick_radius, 0.12; set nb_spheres_size, 0.25; show nb_spheres; set stick_ball, on; set stick_ball_ratio, 1.8;set_view (-0.99,-0.03,0.17,-0.18,0.02,-0.98,0.03,-1.0,-0.03,0.0,0.0,-169.97,8.1,15.62,-1.69,139.24,200.7,-20.0);hide everything, name H*;rock
'''
cmd.reinitialize()
cmd.fetch('3nd4', type='pdb', async='0')
cmd.remove('name H*')
cmd.hide('everything')
cmd.do('run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py')
cmd.do('quat 3nd4')
cmd.bg_color('white')
cmd.do('show stick')
cmd.do('set stick_radius, 0.12')
cmd.do('set nb_spheres_size, 0.25')
cmd.do('show nb_spheres')
cmd.do('set stick_ball, on')
cmd.do('set stick_ball_ratio, 1.8')
cmd.set_view('(-0.96,-0.03,0.3,-0.31,0.02,-0.95,0.03,-1.0,-0.03,0.0,0.0,-231.24,8.16,15.68,-1.66,200.47,262.01,-20.0)')
cmd.rock()
cmd.extend('WC8',WC8)
def N9():
'''
DESCRIPTION
Influenza N9 neuraminidase at 1.55 Angstrom resolution, PDB code
4dgr. The biological unit has four copies of the asymmetric unit.
View is down the four-fold axis. Requires the quat.py script by
Thomas Holder and available at the PyMOL Wiki page. Store quat.py
in ~/Scripts/PyMOLScripts.
USAGE
Type 'N9' to activate. Type 'help N9' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
delete all;
fetch 4dgr, type=pdb, async=0;
run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py;
quat 4dgr;
as cartoon;
bg_color white;
color red, 4dgr_1 and ss H;
color yellow,4dgr_1 and ss S;
color green, 4dgr_1 and ss L+;
color cyan, (not 4dgr_1 and ss H);
color magenta, (not 4dgr_1 and ss S);
color orange, (not 4dgr_1 and ss L+);
set_view (0.98,-0.22,0.01,0.22,0.98,0.02,-0.01,-0.02,1.0,-0.0,0.0,-323.44,1.46,5.33,56.19,274.72,372.15,-20.0);
draw
The commands without linebreaks:
delete all;fetch 4dgr, type=pdb, async=0;run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py; quat 4dgr;as cartoon; bg_color white;color red, 4dgr_1 and ss H;color yellow,4dgr_1 and ss S;color green, 4dgr_1 and ss L+;color cyan, (not 4dgr_1 and ss H);color magenta, (not 4dgr_1 and ss S);color orange, (not 4dgr_1 and ss L+);set_view (0.98,-0.22,0.01,0.22,0.98,0.02,-0.01,-0.02,1.0,-0.0,0.0,-323.44,1.46,5.33,56.19,274.72,372.15,-20.0); draw
'''
cmd.reinitialize()
cmd.fetch('4dgr', type='pdb', async='0')
cmd.do('run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py')
cmd.do('quat 4dgr')
cmd.show_as('cartoon')
cmd.bg_color('white')
cmd.color('red', '4dgr_1 and ss H')
cmd.color('yellow', '4dgr_1 and ss S')
cmd.color('green', '4dgr_1 and ss L+')
cmd.color('cyan', '(not 4dgr_1 and ss H)')
cmd.color('magenta', '(not 4dgr_1 and ss S)')
cmd.color('orange', '(not 4dgr_1 and ss L+)')
cmd.set_view('(0.98,-0.22,0.01,0.22,0.98,0.02,-0.01,-0.02,1.0,-0.0,0.0,-323.44,1.46,5.33,56.19,274.72,372.15,-20.0)')
cmd.draw()
cmd.extend('N9',N9)
def GGT():
'''
DESCRIPTION
WT human gamma glutamyl transpeptidase at 1.67 Angstrom
resolution as cartoon. PDB Code 4gdx.
USAGE
Type 'GGT' to activate. Type 'help GGT' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
delete all;
fetch 4gdx, type=pdb, async=0;
remove name H*;
as cartoon;
bg_color white;
hide (name c+o+n);
set cartoon_side_chain_helper, on;color red, 4gdx and ss H;
color yellow,4gdx and ss S;color green,4gdx and ss L+;
select ASNNAG, resn NAG or resi 95 or i. 120 or i. 230 or
i. 266 or i. 344 or i. 511 or i. 381;
color red, elem o and ASNNAG;
color blue, elem n and ASNNAG;
color yellow, elem c and ASNNAG;
show sticks,ASNNAG;
disable ASNNAG;
set_view (0.55,-0.83,0.07,0.5,0.26,-0.82,0.66,0.49,0.56,0.0,0.0,-197.16,-22.42,-22.69,-12.01,155.44,238.88,-20.0);
draw
The commands without linebreaks:
delete all;fetch 4gdx, type=pdb, async=0;remove name H*;as cartoon;bg_color white; hide (name c+o+n);set cartoon_side_chain_helper, on;color red, 4gdx and ss H; color yellow,4gdx and ss S;color green,4gdx and ss L+; select ASNNAG,resn NAG or resi 95 or i. 120 or i. 230 or i. 266 or i. 344 ori. 511 or i. 381; color red, elem o and ASNNAG; color blue, elem n and ASNNAG;color yellow, elem c and ASNNAG;show sticks,ASNNAG;disable ASNNAG; set_view(0.55,-0.83,0.07,0.5,0.26,-0.82,0.66,0.49,0.56,0.0,0.0,-197.16,-22.42,-22.69,-12.01,155.44,238.88,-20.0); draw
'''
cmd.reinitialize()
cmd.fetch('4gdx', type='pdb', async='0')
cmd.remove('name H*')
cmd.show_as('cartoon')
cmd.bg_color('white')
cmd.hide('(name c+o+n)')
cmd.set('cartoon_side_chain_helper', 'on')
cmd.color('red', '4gdx and ss H')
cmd.color('yellow', '4gdx and ss S')
cmd.color('green', '4gdx and ss L+')
cmd.select('ASNNAG', 'resn NAG or resi 95 or i. 120 or i. 230 or i. 266 or i. 344 or i. 511 or i. 381')
cmd.color('red', 'elem o and ASNNAG')
cmd.color('blue', 'elem n and ASNNAG')
cmd.color('yellow', 'elem c and ASNNAG')
cmd.show('sticks', 'ASNNAG')
cmd.disable('ASNNAG')
cmd.set_view('(0.55,-0.83,0.07,0.5,0.26,-0.82,0.66,0.49,0.56,0.0,0.0,-197.16,-22.42,-22.69,-12.01,155.44,238.88,-20.0)')
cmd.draw()
cmd.extend('GGT',GGT)
def GU():
'''
DESCRIPTION
10-mer dsRNA with 8 contiguous Us. U-helix RNA.
1.32 Angstrom resolution: 4PCO. Has five strands in
the asymmetric unit. Deleted chain E and cobalt
hexammine 102. Cartoon with filled rings and
bases cartoon.
USAGE
Type 'GU' to activate. Type 'help GU' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
delete all;
fetch 4PCO,type=pdb,async=0;
hide everything;
bg_color white;
cartoon oval;
set cartoon_ring_mode, 3;
set cartoon_nucleic_acid_color, blue;
select rna_A, resn A;
select rna_C, resn C;
select rna_G, resn G;
select rna_U, resn U;
color yellow, rna_A;
color red, rna_C;
color gray40, rna_G;
color palecyan, rna_U;
as cartoon;
disable rna_U;
set stick_radius, 0.12;
set nb_spheres_size, 0.3;
show nb_spheres;
set stick_ball, on;
set stick_ball_ratio, 1.8;
show sticks, resn NCO;
show spheres, name Cl;
set_view (0.34,-0.81,0.48,0.89,0.11,
-0.45,0.31,0.58,0.76,-0.0,0.0,-196.36,-9.82,6.76,15.84,159.01,
233.71,-20.0);
draw
The commands without linebreaks:
delete all;fetch 4PCO,type=pdb,async=0;hide everything;bg_color white; cartoon oval;set cartoon_ring_mode, 3;set cartoon_nucleic_acid_color, blue;select rna_A, resn A;select rna_C,resn C;select rna_G, resn G;select rna_U, resn U;color yellow, rna_A; color red, rna_C;color gray40, rna_G; color palecyan, rna_U;as cartoon;disable rna_U; set stick_radius, 0.12;set nb_spheres_size, 0.3; show nb_spheres; set stick_ball, on;set stick_ball_ratio, 1.8; show sticks, resn NCO;show spheres, name Cl; set_view (0.34,-0.81,0.48,0.89,0.11,-0.45,0.31,0.58,0.76,-0.0,0.0,-196.36,-9.82,6.76,15.84,159.01,233.71,-20.0);draw
'''
cmd.reinitialize();
cmd.fetch('4PCO', type='pdb', async='0')
cmd.hide('everything')
cmd.bg_color('white')
cmd.cartoon('oval')
cmd.set('cartoon_ring_mode', '3')
cmd.set('cartoon_nucleic_acid_color', 'blue')
cmd.select('rna_A', 'resn A')
cmd.select('rna_C', 'resn C')
cmd.select('rna_G', 'resn G')
cmd.select('rna_U', 'resn U')
cmd.color('yellow', 'rna_A')
cmd.color('red', 'rna_C')
cmd.color('gray40', 'rna_G')
cmd.color('palecyan', 'rna_U')
cmd.show_as('cartoon')
cmd.disable('rna_U')
cmd.set('stick_radius', '0.12')
cmd.set('nb_spheres_size', '0.3')
cmd.show('nb_spheres')
cmd.set('stick_ball', 'on')
cmd.set('stick_ball_ratio', '1.8')
cmd.show('sticks', 'resn NCO')
cmd.show('spheres', 'name Cl')
cmd.set_view('(0.34,-0.81, 0.48,0.89,0.11,-0.45,0.31,0.58,0.76,-0.0,0.0,-196.36,-9.82,6.76,15.84,159.01,233.71,-20.0)')
cmd.draw()
cmd.extend('GU',GU)
#######Commands to display complex scenes. #############
def BST():
'''
DESCRIPTION
G2G3/U9U8 base step , PDB code 4PCO.
From the 1.32 Angstrom resolution structure
of the RNA decamer with 8 GU base pairs.
USAGE
Type 'BST' to execute. Type 'help BST' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
delete all;
fetch 4PCO, type=pdb, async=0;
select G2G3, ( ((resi 2 or resi 3) and chain A) or ((resi 8 or resi 9) and chain B));
remove not G2G3;
bg_color white;
show sticks;
set stick_radius=0.14;
set stick_ball, on;
set stick_ball_ratio,1.9;
set_view
(-0.75,0.09,0.66,-0.2,0.92,-0.35,-0.64,-0.39,-0.67,-0.0,-0.0,-43.7,7.24,9.55,11.78,29.46,57.91,-20.0);
remove name H*;
select carbon1, element C and (resi 3 or resi 8)
# select lower base pair;
select carbon2, element C and (resi 2 or resi 9)
#select upper base pair;
color gray70, carbon1;
color gray10, carbon2;
show sticks;
space cmyk;
distance hbond1, /4PCO//B/U`9/N3,/4PCO//A/G`2/O6;
distance hbond2, /4PCO//B/U`9/O2,/4PCO//A/G`2/N1;
distance hbond3, /4PCO//A/U`3/N3,/4PCO//B/G`8/O6;
distance hbond4, /4PCO//A/U`3/O2,/4PCO//B/G`8/N1;
color black, hbond1;
color black, hbond2;
color gray70, hbond3;
color gray70, hbond4;
show nb_spheres;
set nb_spheres_size, 0.35;
hide labels;
ray 1600,1000;
png 4PCO.png
Commands without linebreaks:
delete all;fetch 4PCO, type=pdb, async=0;select G2G3, ( ((resi 2 or resi 3) and chain A) or ((resi 8 or resi 9) and chain B));remove not G2G3;bg_color white;show sticks;set stick_radius=0.14;set stick_ball, on;set stick_ball_ratio,1.9;set_view (-0.75,0.09,0.66,-0.2,0.92,-0.35,-0.64,-0.39,-0.67,-0.0,-0.0,-43.7,7. 24,9.55,11.78,29.46,57.91,-20.0);remove name H*;select carbon1, element C and (resi 3 or resi 8);select carbon2, element C and (resi 2 or resi 9);color gray70, carbon1;color gray10, carbon2;show sticks;space cmyk;distance hbond1, /4PCO//B/U`9/N3,/4PCO//A/G`2/O6;distance hbond2, /4PCO//B/U`9/O2,/4PCO//A/G`2/N1;distance hbond3, /4PCO//A/U`3/N3,/4PCO//B/G`8/O6;distance hbond4, /4PCO//A/U`3/O2,/4PCO//B/G`8/N1;color black, hbond1;color black, hbond2;color gray70, hbond3;color gray70, hbond4;show nb_spheres;set nb_spheres_size, 0.35;hide labels;ray 1600,1000;png 4PCO.png
'''
cmd.reinitialize()
cmd.fetch('4PCO', type='pdb', async='0')
cmd.select('G2G3', '( ((resi 2 or resi 3) and chain A)or ((resi 8 or resi 9) and chain B) )')
cmd.remove('not G2G3')
cmd.bg_color('white')
cmd.set('stick_radius', '0.14')
cmd.set('stick_ball', 'on')
cmd.set('stick_ball_ratio', '1.9')
cmd.set_view('(-0.75,0.09,0.66,-0.2,0.92,-0.35,-0.64,-0.39,-0.67,-0.0,-0.0,-43.7,7.24,9.55,11.78,29.46,57.91,-20.0)')
cmd.remove('name H*')
cmd.select('carbon1', 'element C and (resi 3 or resi 8)')
cmd.select('carbon2', 'element C and (resi 2 or resi 9)')
cmd.color('gray70', 'carbon1')
cmd.color('gray10', 'carbon2')
cmd.show('sticks')
cmd.space('cmyk')
cmd.distance('hbond1', '/4PCO//B/U`9/N3', '/4PCO//A/G`2/O6')
cmd.distance('hbond2', '/4PCO//B/U`9/O2', '/4PCO//A/G`2/N1')
cmd.distance('hbond3', '/4PCO//A/U`3/N3', '/4PCO//B/G`8/O6')
cmd.distance('hbond4', '/4PCO//A/U`3/O2', '/4PCO//B/G`8/N1')
cmd.color('black', 'hbond1')
cmd.color('black', 'hbond2')
cmd.color('gray70', 'hbond3')
cmd.color('gray70', 'hbond4')
cmd.show('nb_spheres')
cmd.set('nb_spheres_size', '0.35')
cmd.hide('labels')
cmd.ray('1600', '1000')
cmd.png('4PCO.png')
cmd.extend('BST',BST)
def LG():
'''
DESCRIPTION
Nine sugar glycan in influenza N9 neuraminidase at
1.55 Angstrom resolution, PDB code 4dgr.
The electron density map is contoured at 1.0 sigma.
39 commands were used to make this figure.
USAGE
Type 'LG' to execute. Type 'help LG' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
delete all;
fetch 4dgr, async=0;
fetch 4dgr, type=2fofc,async=0;
select LongGlycan, resi 469:477;
orient LongGlycan;
remove not LongGlycan;
remove name H*;
isomesh 2fofcmap, 4dgr_2fofc, 1, LongGlycan, carve = 1.8;
color density, 2fofcmap;
show sticks;
show spheres;
set stick_radius, .07;
set sphere_scale, .19;
set sphere_scale, .13, elem H;
set bg_rgb=[1, 1, 1];
set stick_quality, 50;
set sphere_quality, 4;
color gray85, elem C;
color red, elem O;
color slate, elem N;
color gray98, elem H;
set stick_color, gray50;
set ray_trace_mode, 1;
set ray_texture, 2;
set antialias, 3;
set ambient, 0.5;
set spec_count, 5;
set shininess, 50;
set specular, 1;
set reflect, .1;
set dash_gap, 0;
set dash_color, black;
set dash_gap, .15;
set dash_length, .05;
set dash_round_ends, 0;
set dash_radius, .05;
set_view (0.34,-0.72,0.61,0.8,0.56,0.22,-0.51,0.4,0.77,0.0,0.0,-81.31,44.64,-9.02,58.62,65.34,97.28,-20.0);
preset.ball_and_stick("all",mode=1);
draw
Commands without linebreaks:
delete all;fetch 4dgr, async=0;fetch 4dgr, type=2fofc, async=0;select LongGlycan, resi 469:477;orient LongGlycan;remove not LongGlycan;remove name H*;isomesh 2fofcmap, 4dgr_2fofc, 1, LongGlycan, carve = 1.8;color density, 2fofcmap; show sticks;show spheres;set stick_radius, .07;set sphere_scale, .19;set sphere_scale, .13, elem H;set bg_rgb=[1, 1, 1];set stick_quality, 50;set sphere_quality, 4;color gray85, elem C;color red, elem O;color slate, elem N;color gray98, elem H;set stick_color, gray50;set ray_trace_mode, 1;set ray_texture, 2;set antialias, 3;set ambient, 0.5;set spec_count, 5;set shininess, 50;set specular, 1;set reflect, .1;set dash_gap, 0;set dash_color, black;set dash_gap, .15;set dash_length, .05;set dash_round_ends, 0;set dash_radius, .05;set_view (0.34,-0.72,0.61,0.8,0.56,0.22,-0.51,0.4,0.77,0.0,0.0,-81.31,44.64,-9.02,58.62,65.34,97.28,-20.0);preset.ball_and_stick("all",mode=1);draw
'''
cmd.reinitialize()
cmd.fetch('4dgr', async='0')
cmd.fetch('4dgr', type='2fofc', async='0')
cmd.select('LongGlycan', 'resi 469:477')
cmd.orient('LongGlycan')
cmd.remove('not LongGlycan')
cmd.remove('name H*')
cmd.isomesh('2fofcmap', '4dgr_2fofc', '1', 'LongGlycan', carve ='1.8')
cmd.color('density', '2fofcmap')
cmd.show('sticks')
cmd.show('spheres')
cmd.set('stick_radius', '.07')
cmd.set('sphere_scale', '.19')
cmd.set('sphere_scale', '.13', 'elem H')
cmd.set('bg_rgb', '[1, 1, 1]')
cmd.set('stick_quality', '50')
cmd.set('sphere_quality', '4')
cmd.color('gray85', 'elem C')
cmd.color('red', 'elem O')
cmd.color('slate', 'elem N')
cmd.color('gray98', 'elem H')
cmd.set('stick_color', 'gray50')
cmd.set('ray_trace_mode', '1')
cmd.set('ray_texture', '2')
cmd.set('antialias', '3')
cmd.set('ambient', '0.5')
cmd.set('spec_count', '5')
cmd.set('shininess', '50')
cmd.set('specular', '1')
cmd.set('reflect', '.1')
cmd.set('dash_gap', '0')
cmd.set('dash_color', 'black')
cmd.set('dash_gap', '.15')
cmd.set('dash_length', '.05')
cmd.set('dash_round_ends', '0')
cmd.set('dash_radius', '.05')
cmd.set_view('(0.34,-0.72,0.61,0.8,0.56,0.22,-0.51,0.4,0.77,0.0,0.0,-81.31,44.64,-9.02,58.62,65.34,97.28,-20.0)')
preset.ball_and_stick("all",mode=1);
cmd.draw()
cmd.extend('LG',LG)
def NA():
'''
DESCRIPTION
Hydrated sodium cation bound in major groove of a
16-mer RNA of Watson-Crick base pairs.
The sodium is bound to the N7 nitrogen atom of
Adenine 3 at 1.55 Angstrom resolution, PDB code 3nd4.
57 commands were used to make this figure.
More than one label in a horizontal script is not
allowed. This one label has to be at the end of the line.
Labels can be imported from a Labels.pml file.
Store the label commands one per row in this file.
Import the file with the @Labels.pml command.
Include the path to the file if the labels file is not
in the current working directory of PyMOL.
USAGE
Type 'NA' to execute. Type 'help NA' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
delete all;
viewport 900,600;
fetch 3nd4, type=pdb, async=0;
run ~/Scripts/PyMOLScripts/quat.py;
quat 3nd4;
show sticks;
set stick_radius=0.125;
hide everything, name H*;
bg_color white;
create coorCov, (3nd4_1 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)));
bond (coorCov//A/NA`19/NA),(coorCov//A/A`3/N7);
bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`119/O);
bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`219/O);
bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`319/O);
bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`419/O);
bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`519/O);
distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 519);
distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 419);
distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 119);
distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 319);
distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 219);
show nb_spheres;
set nb_spheres_size, .35;
distance hbond1,/3nd4_1/1/A/HOH`119/O, /3nd4_1/1/A/A`3/OP2;
distance hbond2,/3nd4_1/1/A/HOH`319/O,/3nd4_1/1/A/A`3/OP2;
distance hbond3,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/HOH`119/O;
distance hbond4,/3nd4_1/1/A/G`4/N7,/3nd4_1/1/A/HOH`91/O;
distance hbond5,/3nd4_1/1/A/G`4/O6, /3nd4_1/1/A/HOH`419/O;
distance hbond6,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2;
distance hbond7,/3nd4_1/1/A/HOH`319/O,/3nd4_1/1/A/G`2/OP2;
distance hbond9,/3nd4_1/1/A/HOH`419/O,/3nd4_2/2/A/HOH`74/O;
distance hbond10,/3nd4_2/2/A/C`15/O2,/3nd4_1/1/A/G`2/N2;
distance hbond11, /3nd4_2/2/A/C`15/N3,/3nd4_1/1/A/G`2/N1;
distance hbond12,/3nd4_2/2/A/C`15/N4,/3nd4_1/1/A/G`2/O6;
distance hbond13, /3nd4_2/2/A/U`14/N3,/3nd4_1/1/A/A`3/N1;
distance hbond14,3nd4_2/2/A/U`14/O4,/3nd4_1/1/A/A`3/N6;
distance hbond15, /3nd4_2/2/A/C`13/N4,/3nd4_1/1/A/G`4/O6;
distance hbond16,/3nd4_2/2/A/C`13/N3, /3nd4_1/1/A/G`4/N1;
distance hbond17, /3nd4_1/1/A/G`4/N2,/3nd4_2/2/A/C`13/O2;
distance hbond18,/3nd4_1/1/A/G`2/N2,/3nd4_2/2/A/C`15/O2;
distance hbond19,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2;
set depth_cue=0;
set ray_trace_fog=0;
set dash_color, black;
set label_font_id, 5;
set label_size, 36;
set label_position, (0.5, 1.0, 2.0);
set label_color, black;
set dash_gap, 0.2;
set dash_width, 2.0;
set dash_length, 0.2;
set label_color, black;
set dash_gap, 0.2;
set dash_width, 2.0;
set dash_length, 0.2;
select carbon, element C;
color yellow, carbon;
disable carbon;
set_view (-0.9,0.34,-0.26,0.33,0.18,-0.93,-0.27,-0.92,-0.28,-0.07,-0.23,-27.83,8.63,19.85,13.2,16.0,31.63,-20.0)
The commands without linebreaks:
delete all;viewport 900,600;fetch 3nd4, type=pdb,async=0;run ~/Scripts/PyMOLScripts/quat.py;quat 3nd4; show sticks;set stick_radius=0.125;hide everything, name H*;bg_color white;create coorCov, (3nd4_1 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)));bond (coorCov//A/NA`19/NA),(coorCov//A/A`3/N7); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`119/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`219/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`319/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`419/O); bond (coorCov//A/NA`19/NA),(coorCov//A/HOH`519/O);distance (3nd4_1 and chain Aand resi 19 and name NA), (3nd4_1 and chain A and resi 519);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 419);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 119);distance (3nd4_1 and chain A and resi 19 and name NA),(3nd4_1 and chain A and resi 319);distance (3nd4_1 and chain A and resi 19 and name NA), (3nd4_1 and chain A and resi 219);show nb_spheres; set nb_spheres_size, .35;distance hbond1,/3nd4_1/1/A/HOH`119/O, /3nd4_1/1/A/A`3/OP2;distance hbond2,/3nd4_1/1/A/HOH`319/O, /3nd4_1/1/A/A`3/OP2;distance hbond3,/3nd4_1/1/A/HOH`91/O, /3nd4_1/1/A/HOH`119/O;distance hbond4,/3nd4_1/1/A/G`4/N7,/3nd4_1/1/A/HOH`91/O;distance hbond5,/3nd4_1/1/A/G`4/O6, /3nd4_1/1/A/HOH`419/O;distance hbond6,/3nd4_1/1/A/HOH`91/O, /3nd4_1/1/A/G`4/OP2;distance hbond7,/3nd4_1/1/A/HOH`319/O, /3nd4_1/1/A/G`2/OP2;distance hbond9,/3nd4_1/1/A/HOH`419/O,/3nd4_2/2/A/HOH`74/O;distance hbond10,/3nd4_2/2/A/C`15/O2,/3nd4_1/1/A/G`2/N2;distance hbond11, /3nd4_2/2/A/C`15/N3,/3nd4_1/1/A/G`2/N1;distance hbond12,/3nd4_2/2/A/C`15/N4,/3nd4_1/1/A/G`2/O6;distance hbond13, /3nd4_2/2/A/U`14/N3,/3nd4_1/1/A/A`3/N1;distance hbond14,3nd4_2/2/A/U`14/O4,/3nd4_1/1/A/A`3/N6;distance hbond15, /3nd4_2/2/A/C`13/N4,/3nd4_1/1/A/G`4/O6;distance hbond16,/3nd4_2/2/A/C`13/N3, /3nd4_1/1/A/G`4/N1;distance hbond17, /3nd4_1/1/A/G`4/N2,/3nd4_2/2/A/C`13/O2;distance hbond18,/3nd4_1/1/A/G`2/N2,/3nd4_2/2/A/C`15/O2;distance hbond19,/3nd4_1/1/A/HOH`91/O,/3nd4_1/1/A/G`4/OP2;set depth_cue=0;set ray_trace_fog=0;set dash_color, black;set label_font_id, 5;set label_size, 36;set label_position, (0.5, 1.0, 2.0);set label_color, black;set dash_gap, 0.2;set dash_width, 2.0;set dash_length, 0.2;set label_color, black;set dash_gap, 0.2;set dash_width, 2.0;set dash_length, 0.2;select carbon, element C; color yellow, carbon;disable carbon;set_view (-0.9,0.34,-0.26,0.33,0.18,-0.93,-0.27,-0.92,-0.28,-0.07,-0.23,-27.83,8.63,19.85,13.2,16.0,31.63,-20.0);
'''
cmd.reinitialize();
cmd.viewport('900','600');
cmd.fetch('3nd4', type='pdb', async='0');
cmd.do('run /Users/blaine-mooers/Scripts/PyMOLScripts/quat.py')
cmd.do('quat 3nd4');
cmd.show('sticks');
cmd.set('stick_radius', '0.125');
cmd.hide('everything', 'name H*');
cmd.bg_color('white');
cmd.create('coorCov', '(3nd4_1 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)))');
cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/A`3/N7)');
cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/HOH`119/O)');
cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/HOH`219/O)');
cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/HOH`319/O)');
cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/HOH`419/O)');
cmd.bond('(coorCov//A/NA`19/NA)','(coorCov//A/HOH`519/O)');
cmd.distance('(3nd4_1 and chain A and resi 19 and name NA)','(3nd4_1 and chain A and resi 519)');
cmd.distance('(3nd4_1 and chain A and resi 19 and name NA)','(3nd4_1 and chain A and resi 419)');
cmd.distance('(3nd4_1 and chain A and resi 19 and name NA)','(3nd4_1 and chain A and resi 119)');
cmd.distance('(3nd4_1 and chain A and resi 19 and name NA)','(3nd4_1 and chain A and resi 319)');
cmd.distance('(3nd4_1 and chain A and resi 19 and name NA)','(3nd4_1 and chain A and resi 219)');
cmd.show('nb_spheres');
cmd.set('nb_spheres_size', '.35');
cmd.distance('hbond1', '/3nd4_1/1/A/HOH`119/O', '/3nd4_1/1/A/A`3/OP2');
cmd.distance('hbond2', '/3nd4_1/1/A/HOH`319/O', '/3nd4_1/1/A/A`3/OP2');
cmd.distance('hbond3', '/3nd4_1/1/A/HOH`91/O', '/3nd4_1/1/A/HOH`119/O');
cmd.distance('hbond4', '/3nd4_1/1/A/G`4/N7', '/3nd4_1/1/A/HOH`91/O');
cmd.distance('hbond5', '/3nd4_1/1/A/G`4/O6', '/3nd4_1/1/A/HOH`419/O');
cmd.distance('hbond6', '/3nd4_1/1/A/HOH`91/O', '/3nd4_1/1/A/G`4/OP2');
cmd.distance('hbond7', '/3nd4_1/1/A/HOH`319/O', '/3nd4_1/1/A/G`2/OP2');
cmd.distance('hbond9', '/3nd4_1/1/A/HOH`419/O', '/3nd4_2/2/A/HOH`74/O');
cmd.distance('hbond10', '/3nd4_2/2/A/C`15/O2', '/3nd4_1/1/A/G`2/N2');
cmd.distance('hbond11', '/3nd4_2/2/A/C`15/N3', '/3nd4_1/1/A/G`2/N1');
cmd.distance('hbond12', '/3nd4_2/2/A/C`15/N4', '/3nd4_1/1/A/G`2/O6');
cmd.distance('hbond13', '/3nd4_2/2/A/U`14/N3', '/3nd4_1/1/A/A`3/N1');
cmd.distance('hbond14', '/3nd4_2/2/A/U`14/O4', '/3nd4_1/1/A/A`3/N6');
cmd.distance('hbond15', '/3nd4_2/2/A/C`13/N4', '/3nd4_1/1/A/G`4/O6');
cmd.distance('hbond16', '/3nd4_2/2/A/C`13/N3', '/3nd4_1/1/A/G`4/N1');
cmd.distance('hbond17', '/3nd4_1/1/A/G`4/N2', '/3nd4_2/2/A/C`13/O2');
cmd.distance('hbond18', '/3nd4_1/1/A/G`2/N2', '/3nd4_2/2/A/C`15/O2');
cmd.distance('hbond19', '/3nd4_1/1/A/HOH`91/O', '/3nd4_1/1/A/G`4/OP2');
cmd.set('depth_cue', '0');
cmd.set('ray_trace_fog', '0');
cmd.set('dash_color', 'black');
cmd.set('label_font_id', '5');
cmd.set('label_size', '36')
cmd.set('label_position', '(0.5, 1.0,2.0)');
cmd.set('label_color', 'black');
cmd.set('dash_gap', '0.2');
cmd.set('dash_width', '2.0');
cmd.set('dash_length', '0.2');
cmd.set('label_color', 'black');
cmd.set('dash_gap', '0.2');
cmd.set('dash_width', '2.0');
cmd.set('dash_length', '0.2');
cmd.select('carbon', 'element C');
cmd.color('yellow', 'carbon');
cmd.disable('carbon');
cmd.set_view('-0.9,0.34,-0.26,0.33,0.18,-0.93,-0.27,-0.92,-0.28,-0.07,-0.23,-27.83,8.63,19.85,13.2,16.0,31.63,-20.0');
cmd.extend('NA',NA)
# ##### Commands applicable to displayed molecules. ##########
def AO():
'''
DESCRIPTION
Commands to make ambient occlusion image like those in Qutemole.
USAGE
Type 'AO' to execute. Type 'help AO' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the comand line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
set_color oxygen, [1.0,0.4,0.4];
set_color nitrogen, [0.5,0.5,1.0];
remove solvent;
as spheres;
util.cbaw;
bg white;
set light_count,10;
set spec_count,1;
set shininess, 10;
set specular,0.25;
set ambient,0;
set direct,0;
set reflect,1.5;
set ray_shadow_decay_factor, 0.1;
set ray_shadow_decay_range, 2;
unset depth_cue;
ray
The commands without linebreaks:
set_color oxygen, [1.0,0.4,0.4];set_color nitrogen, [0.5,0.5,1.0];remove solvent;as spheres;util.cbaw;bg white;set light_count,10;set spec_count,1;set shininess, 10;set specular,0.25;set ambient,0;set direct,0;set reflect,1.5;set ray_shadow_decay_factor, 0.1;set ray_shadow_decay_range, 2;unset depth_cue;ray
'''
cmd.set_color('oxygen', '[1.0,0.4,0.4]')
cmd.set_color('nitrogen', '[0.5,0.5,1.0]')
cmd.remove('solvent')
cmd.show_as('spheres')
cmd.util.cbaw()
cmd.bg_color('white')
cmd.set('light_count', '10')
cmd.set('spec_count', '1')
cmd.set('shininess', '10')
cmd.set('specular', '0.25')
cmd.set('ambient', '0')
cmd.set('direct', '0')
cmd.set('reflect', '1.5')
cmd.set('ray_shadow_decay_factor', '0.1')
cmd.set('ray_shadow_decay_range', '2')
cmd.unset('depth_cue')
cmd.ray()
cmd.extend('AO',AO)
def BW():
'''
DESCRIPTION
Commands to make black-and white-ribbon cartoon on a white background.
Good for avoiding color figure charges. Requires a pdb file. Can cause PyMOL
to crash if applied to a cartoon representation. Best applied while object is
still shown as lines.
USAGE
Orient struture as desired. Then type 'BW' to execute the function. Type
'help BW' to see this documentation printed to the command history window.
Select from the command history individual lines of code to build a new
script. Select the hortizontal script at the bottom if retaining most of
the commands in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.
The commands with linebreaks:
show cartoon;
hide lines;
hide nonbonded;
# black and white cartoon;
# note how the dcomment is on a separate line and not to the right of a command;
set ray_trace_mode, 2;
bg_color white;
set antialias, 2;
ray 1600,1600;
png test.png
Commands without linebreaks:
show cartoon; hide lines; hide nonbonded; set ray_trace_mode, 2; # black and white cartoon; bg_color white; set antialias, 2; ray 1600,1600; png test.png
'''
cmd.show_as("cartoon", "all");
cmd.hide('lines');
cmd.hide('nonbonded');
# black and white cartoon;
cmd.set('ray_trace_mode', '2');
cmd.bg_color('white');
cmd.set('antialias', '2');
cmd.ray('600','600');
cmd.png('test.png')
cmd.extend('BW',BW)
def BU():
'''
DESCRIPTION
Commands to make biological unit. Requires a pdb file. There are
other ways of displaying the biological unit in PyMOL. Depends on
the quat.py script by Thomas Holder.
USAGE
Type 'BU' to execute. Type 'help BU' to see this documentation
printed to the command history window. Select from the command
history individual lines of code to build a new script. Select the
hortizontal script at the bottom if retaining most of the commands
in your new script. Copy and paste onto the command line below.
Works only with the command line immediately under the command
history window at the top of the gui.