Useful VMD skills.

This is got from http://www.life.umd.edu/biology/sukharevlab/download/vmd_scripts/vmd_enhanced_startup_file.htm#Text Commands.

“Shift” key is also useful when you want to rotate the selected molecular.

 Hot Keys (for OpenGL Window): 

Mouse mode 

R	enter rotate mode; stop rotation
T	enter translate mode
S	enter scaling mode
C	assign rotation center
0	query item; show labels menu
1	pick atom
2	pick bond (2 atoms)
3	pick angle (3 atoms)
4	pick dihedral (4 atoms)
5	move atom
6	move residue
7	move fragment
8	move molecule
9	move highlighted rep

View 

Q	view from positive direction of x axis	 (|||screenshot)
W	view from positive direction of y axis	 (|||screenshot)
E	view from positive direction of z axis	 (|||screenshot)
F	flip view 180º (view from the back of the current view)
X	spin about x axis
Y	spin about y axis
Z	spin about z axis
J	rotate 2º about x
K	rotate -2º about x
L	rotate 2º about y
H	rotate -2º about y

Representations 

N	apply preselected graphical representation (new ribbons colored by index)   (|||screenshot)
I	apply preselected graphical representation (trace colored by index)   (|||screenshot)
V	set white background and 'exp2' depth cue   (|||screenshot)
B	set black background without depthcue
P	switch depthcue on and off
U	make the selections of the top molecule to auto update each frame
A	apply representations from the top molecule to all other molecules.
	Based on save_state script by John Stone.

Additional graphics 

O (o)	draw coordinate cylinders in origin (red x, green y, blue z)   (|||screenshot)
G	draw coordinate greed (red x, green y, blue z). One tick 1Å, small
	square 5Å, big square 10Å. The whole greed is +- 100 A. It looks neat when used
	with view from x, y, or z directions (buttons Q,W,E)   (|||screenshot)
D	remove all the graphics added

Menus 

[	show main menu   (|||screenshot)
]	show files menu, and set the current folder as of the top molecule file  (|||screenshot)
'	show graphics (Graphical Representations) menu  (|||screenshot)
\	show sequence menu  (|||screenshot)
;	show tkcon Tcl console (Works after the first use of Extensions -> tkcon)  (|||screenshot)

Animation 

+	move to next frame
-	move to previous frame
. >	play animation forward
, <	play animation reverse
/ ?	stop animation

Modifications 

M	move geometry center of the molecule to the origin
` ~	orient top molecule (not more than 50,000 atoms) by principal axes
	(requires Orient script written by Paul Grayson and requires linear algebra
	package by Hume Integration Software)  (|||screenshot)

 Text Commands (for the console): 

h	Show this list of Hot keys and Text commands

a	Loads coordinates from the filelist and adds them as new frames to the top molecule
	Syntax: a {file1.coor file2.pdb file3.dcd}; a {c:/temp} {file1.dcd} 10
	Filenames can be separated by new lines. First argument can be path to files, it can be
	omitted or empty. The third argument can be step for trajectory reading or can be omitted.
	Filename can include full path.

n	Loads coordinates from the filelist and adds them as new files.
	Syntax: n {file1.coor file2.pdb file3.dcd}; n {c:/temp} {file1.dcd} 10
	Filenames can be separated by new lines. First argument can be path to files, it can be
	omitted or empty. The third argument can be step for trajectory reading or can be omitted.

t	sets current working folder to 'C:/Temp'

c	sets current working folder to the path to the first loaded file of the top molecule

pdb	Write current frame of the top file to a pdb file <old_name>_.pdb

fx	Rotate (flip) protein 180 degrees around x axis (changes coordinates)

fy	Rotate (flip) protein 180 degrees around y axis (changes coordinates)

fz	Rotate (flip) protein 180 degrees around z axis (changes coordinates)

colstart	Starts collaboration session between two VMD machines
		Based on Justin Gullingsrud's vmdcollab script

colstop 	Stops collaboration session between two VMD machines
		Based on Justin Gullingsrud's vmdcollab script

betascale	Sets beta value of protein residues to the value found in the
	 selected hydrophobicity scale.   (|||screenshot)
	 Usage: 'betascale' - prints the list of
	 scales; 'betascale <scale_name>' - assigns values from the scale ; 
	 'betascale <scale_name> scale' -  assigns values from the scale and 
	 prints scale values on the console screen. 
	 Most of the scales are taken from the ExPASy ProtScale page.

bs	Same as 'betascale'

mutant	Creates mutant of the protein from the current structure using PSFGEN.   (|||screenshot)
	Usage: 'mutant <resnum> <mutant_restype>' E.g.: 'mutant 109 THR 115 VAL'
morph	Adds frames with linear interpolation between the existing frames of the top 
	molecule. Usage: 'morph <frames_increase_factor> <frames_insertion_frequency_type>'
	or 'morph <start:frames_increase_factor:end> <frames_insertion_frequency_type>'
	E.g. 'morph 10' 'morph 2 linear' 'morph 3 cycle' 'morph 100 sin2' 'morph 3:10:4 linear'
	based on the "morph 1.0" by Andrew Dalke (dalke@ks.uiuc.edu), and modified 
	to handle the trajectory with any number of frames
cell	Sets the cell size for periodic images. 
	Usage: cell <{Specified a, b, c, alpha, beta, gamma}|{line from xsc file}|{cell
	parameters from NAMD configuration}|{xsc filename}>
	E.g. 'cell {100 110 120 90 90 60}' 'cell {sim-mscs-007.xsc}'
symm	calculate symmetric structure closest to the starting structure of homooligomer,
 	or spread conformation of one monomer onto the whole oligomer.  (|||screenshot)
 	Usage: symm <|"selection_string"> <|monomer_index|symmetrization_mode>.
 	monomer_index: integer 0 to (number_of_monomers - 1)
 	symmetrization_mode: 'avg' - average, 'max' - the most different monomer, 
 	'min' - monomer closest to the average. E.g. 'symm' 'symm "resid 23"'
 	'symm min' 'symm max' 'symm avg' 'symm "resid 23" 0'
 	'symm' is equivalent to 'symm "protein" max'
radii	sets atomic VDW radii according to the values read from the predefined values,
	 or from file with atom types and radii, or from CHARMM parameters file.  (|||screenshot)
	Syntax: radii {}  ==> Displays brief help and sets predefined CHARMM radii
        radii v  ==> restores default VMD radii
        radii {c:/path/param_charmm.inp}  ==> reads radii from CHARMM parameters file
        radii {c:/path/raddi_file.txt} r  ==> reads radii from 'type TAB radius' file
ss	starts sscache script recalculating secondary structure for every frame and keeping it
	in the cache for fast use. Based on the sscache script by Andrew Dalke 
	(dalke@ks.uiuc.edu)
	Usage: ss <molid|top|>. E.g. 'ss', 'ss top', 'ss 2' 
lbl	Labels each atom in the 'selectionText' with information 'labelInfo', with 
	arbitrary prefix 'labelPrefix', color 'color' and font size 'size' (default 1).  (|||screenshot)
	Syntax:  'lbl <|selectionText> <|labelInfo> <|labelPrefix> <|color> <|size>' 
	E.g. 'lbl {resid 1 to 10 and name CA}', 
	'lbl {name CA} {resname resid} { } blue 0.5'
Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s