.vmdrc

# -*- tcl -*-
############################################################################
#cr
#cr            (C) Copyright 1995 The Board of Trustees of the
#cr                        University of Illinois
#cr                         All Rights Reserved
#cr
############################################################################

############################################################################
# RCS INFORMATION:
#
#       $RCSfile: .vmdrc,v $
#       $Author: johns $        $Locker:  $                $State: Exp $
#       $Revision: 1.5 $      $Date: 2000/05/23 16:00:17 $
#
############################################################################
# DESCRIPTION:
#
# VMD startup script.  The commands here are executed as soon as VMD starts up
############################################################################
# Modified by Andriy Anishkin (anishkin@icqmail.com) UMCP
# Found online here: http://www.life.umd.edu/biology/sukharevlab/download/vmd_scripts/vmd.rc

#Modified by Chris MacDermaid (chris.macdermaid@gmail.com) UPENN Aug 2008.

# turn on lights 0 and 1
light 0 on
light 1 on
light 2 off
light 3 off
display nearclip set 0

# position the stage and axes
#axes location lowerleft
axes location off
stage location off

# position and turn on menus
menu main     move 1681 512
menu animate  move 125  30
menu edit     move 125  225
menu tracker  move 125  520
menu display  move 395  30
menu graphics move 250 512
menu color    move 125  225
menu files    move 2150 512
menu molecule move 0    512
menu labels   move 661  29
menu render   move 125  525
menu sequence move 629  0

# # position and turn on menus
# menu main     move 7   785
# menu animate  move 125 30
# menu edit     move 125 225
# menu tracker  move 125 520
# menu display  move 395 30
# menu graphics move 912 332
# menu color    move 125 225
# menu files    move 825 502
# menu molecule move 125 525
# menu labels   move 912 29
# menu render   move 125 525
# menu sequence move 881 0

menu main     on
#menu animate  on
#menu edit     on
#menu tracker  on
#menu display  on
menu graphics on
#menu color    on
#menu labels   on
#menu renderer on
#menu molecule on
menu files    on

after idle {

    if {![info exists env(VMDTEXT)]} {
        menu tkcon on
        menu tkcon move 250 250
    }

    vmdrestoremycolors

    ## Load scripts in vmd.d
    foreach f [glob -directory $env(HOME)/.vmd.d *.tcl] {
        puts "Loading file $f"
        source $f
    }

    ## Colorscale
    setcolors vmd_0.75 ;#Drop the saturation of the default colors
    setcolorscale jet  ;#Set the colorscale to Matlab's jet

    color Name C green
    color Type C green
    color change rgb 0 0.1 0.2 0.7 ;# blue
    color change rgb 1 0.7 0.2 0.1 ;# red
    color change rgb 3 0.7 0.4 0.0 ;# orange
    color change rgb 4 0.8 0.7 0.1 ;# yellow
    color change rgb 7 0.1 0.7 0.2 ;# green

    foreach p {topotools qwrap cg} {
      catch {package require $p}
    }
}

display projection orthographic

# +-------------------------+
# | Autoload custom plugins |
# +-------------------------+
set auto_path [linsert $auto_path 0 [file join $env(HOME) .vmdplugins]]

## Set a standard property lookup variable for atomselect
set proplist {name type mass charge radius element resname resid chain segname}

proc h { } {
    # Prints help for keyboard shortcuts to the screen
    puts "
______________________ 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
W   view from positive direction of y axis
E   view from positive direction of z axis
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 chain)
I   apply preselected graphical representation (trace colored by index)
V   set white background and 'exp2' depth cue
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

___ Additional graphics ___
O (o)   draw coordinate cylinders in origin (red x, green y, blue z)
G   draw coordinate greed (red x, green y, blue z). One tick 1A, small
square 5A, big square 10A.
D   remove all the graphics added


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


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


___ Modifications ___
i   move geometry center of the molecule to the origin

______________________ 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.
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)
betascale   Sets beta value of protein residues to the value found in the
selected hydrophobicity scale.
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
bs  Same as 'betascale'

}

user add key {O} {
    #Reset Display
    display projection orthographic
}

user add key {P} {
    #Reset Display
    display projection perspective
}

user add key {*} {
    #Reset Display
    display resetview
}

user add key {=} {
    #goes to the next animation frame
    animate next
}

user add key f {
    #Flips  -  Rotates scene 180 degrees aroynd Y (vertical on screen) axis
    rotate y by 180
}


user add key q {
    #Rotates scene to make a view from X axis, z is up
    mouse stoprotation
    rotate x to -90
    rotate y by -90
}

user add key w {
    #Rotates scene to make a view from Y axis, z is up
    mouse stoprotation
    rotate z to 180
    rotate x by -90
}

user add key e {
    #Rotates scene to make a view from Z axis, x is to the left
    mouse stoprotation
    rotate z to 180
}

user add key o {
    #draws coordinate cylinders in origin
    draw color red
    draw cylinder {-100 0 0} {100 0 0} radius 0.5
    draw cone {2 0 0} {5 0 0} radius 1 resolution 12
    draw color green
    draw cylinder {0 -100 0} {0 100 0} radius 0.5
    draw cone {0 2 0} {0 5 0} radius 1 resolution 12
    draw color blue
    draw cylinder {0 0 -100} {0 0 100} radius 0.5
    draw cone {0 0 2} {0 0 5} radius 1 resolution 12

}

user add key d {
    #removes all the graphics added
    draw delete all
}

user add key g {
    draw color red
    draw cylinder {-100 0 0} {100 0 0} radius 0.5
    draw cone {2 0 0} {5 0 0} radius 1 resolution 12
    draw color green
    draw cylinder {0 -100 0} {0 100 0} radius 0.5
    draw cone {0 2 0} {0 5 0} radius 1 resolution 12
    draw color blue
    draw cylinder {0 0 -100} {0 0 100} radius 0.5
    draw cone {0 0 2} {0 0 5} radius 1 resolution 12

    for {set i -100} {$i <= 100} {incr i} {
        draw color red
        set v1 "-1 $i 0"
        set v2 "1 $i 0"
        set v3 "-1 0 $i"
        set v4 "1 0 $i"
        draw cylinder $v1 $v2 radius 0.05
        draw cylinder $v3 $v4 radius 0.05
        draw color green
        set v1 "0 -1 $i"
        set v2 "0 1 $i"
        set v3 "$i -1 0"
        set v4 "$i 1 0"
        draw cylinder $v1 $v2 radius 0.05
        draw cylinder $v3 $v4 radius 0.05
        draw color blue
        set v1 "$i 0 -1"
        set v2 "$i 0 1"
        set v3 "0 $i -1"
        set v4 "0 $i 1"
        draw cylinder $v1 $v2 radius 0.05
        draw cylinder $v3 $v4 radius 0.05
    }

    for {set i -20} {$i <= 20} {incr i} {
        draw color red
        set v1 "-100 [expr ($i*5)] 0"
        set v2 "100 [expr ($i*5)] 0"
        set v3 "-100 0 [expr ($i*5)]"
        set v4 "100 0 [expr ($i*5)]"
        draw cylinder $v1 $v2 radius 0.1
        draw cylinder $v3 $v4 radius 0.1
        draw color green
        set v1 "0 -100 [expr ($i*5)]"
        set v2 "0 100 [expr ($i*5)]"
        set v3 "[expr ($i*5)] -100 0"
        set v4 "[expr ($i*5)] 100 0"
        draw cylinder $v3 $v4 radius 0.1
        draw cylinder $v1 $v2 radius 0.1
        draw color blue
        set v1 "[expr ($i*5)] 0 -100"
        set v2 "[expr ($i*5)] 0 100"
        set v3 "0 [expr ($i*5)] -100"
        set v4 "0 [expr ($i*5)] 100"
        draw cylinder $v3 $v4 radius 0.1
        draw cylinder $v1 $v2 radius 0.1
    }

    for {set i -10} {$i <= 10} {incr i} {
        draw color red
        set v1 "-100 [expr ($i*10)] 0"
        set v2 "100 [expr ($i*10)] 0"
        set v3 "-100 0 [expr ($i*10)]"
        set v4 "100 0 [expr ($i*10)]"
        draw cylinder $v1 $v2 radius 0.2
        draw cylinder $v3 $v4 radius 0.2
        draw color green
        set v1 "0 -100 [expr ($i*10)]"
        set v2 "0 100 [expr ($i*10)]"
        set v3 "[expr ($i*10)] -100 0"
        set v4 "[expr ($i*10)] 100 0"
        draw cylinder $v1 $v2 radius 0.2
        draw cylinder $v3 $v4 radius 0.2
        draw color blue
        set v1 "[expr ($i*10)] 0 -100"
        set v2 "[expr ($i*10)] 0 100"
        set v3 "0 [expr ($i*10)] -100"
        set v4 "0 [expr ($i*10)] 100"
        draw cylinder $v3 $v4 radius 0.2
        draw cylinder $v1 $v2 radius 0.2
    }
}




user add key i {
    #Moves geometry center of the molecule to the origin
    set sel999 [atomselect top all]
    $sel999 moveby [vecscale -1.0 [measure center $sel999]]
    $sel999 delete
}


# +-----------------+
# | REPRESENTATIONS |
# +-----------------+


#Apply preselected graphical representation

set numreps 0
set selrep 0
set repstat 0
set numreptype 6

proc changerep {repstat} {
    global numreps selrep

    #   mol delrep $numreps top

    switch $repstat {
        0 {
            mol modstyle $selrep top Licorice 0.2 10 10
            mol modcolor $selrep top Name

        }
        1 {
            mol modstyle $selrep top NewRibbons 1.800000 6.000000 2.600000 0
            mol modcolor $selrep top Chain
        }
        2 {
            mol modstyle $selrep top Licorice 0.2 10 10
            mol modcolor $selrep top ResType
        }
        3 {
            mol modstyle $selrep top Trace 0.500000 6.000000
            mol modcolor $selrep top Index
        }
        4 {
            mol modstyle $selrep top vdw
            mol modcolor $selrep top ResType
        }
        5 {
            mol modstyle $selrep top lines
            mol modcolor $selrep top Name
        }
        6 {
            mol modstyle $selrep top QuickSurf
            mol modcolor $selrep top Name
        }
        7 {
        }
        default {
            mol modstyle $selrep top lines
            mol modcolor $selrep top Name
        }
    }

    if {$numreps < 0} {set numreps 0}
}


# m/M are toggles m --> New Rep, M --> del Rep

user add key m {

    mol addrep top
    incr numreps

    if {$numreps > 0} { incr selrep }
}

user add key M {

    mol delrep $selrep top
    if {$numreps > -1} {
        set numreps [expr {$numreps - 1}]
        if {$selrep > 0} { set selrep [ expr {$selrep - 1} ] }
    }
}

# n/N are toggles N --> Next Rep, n --> Prev Rep

user add key n {
    if {$repstat <= 0} {
        set repstat $numreptype
    } else {
        set repstat [ expr {$repstat - 1} ]
    }

    changerep $repstat
}

user add key N {
    if {$repstat >= $numreptype} {
        set repstat 0
    } else {
        incr repstat
    }

    changerep $repstat
}

## Cycle Active Representations

user add key b {
    if {$selrep < $numreps} {
        incr selrep
    } else {
        set selrep 0
    }
    puts "Selection: $selrep"
}

user add key B {
    if {$selrep > 0} {
        set selrep [ expr {$selrep - 1} ]
    } elseif {$numreps <= 0} {
        set selrep 0
    } else {
        set selrep $numreps
    }
    puts "Selection: $selrep"
}

user add key 0 {
    mouse mode 4 0
    menu labels on
}


user add key v {
    #sets white background and exp2 depth cue
    color Display {Background} white

    display depthcue   on
    display cuestart   0.500000
    display cueend     10.000000
    display cuedensity 0.400000
    display cuemode    Exp2
}

user add key V {
    #sets black background without depthcue
    color Display {Background} black

    display depthcue   off
}

user add key p {
    #switches depthcue on and off
    if {[string compare [display get depthcue] on] == 0} {
        #Switch depthcue off
        display depthcue off
    } {
        #Switch depthcue on
        display depthcue   on
        #       display cuestart   0.500000
        #       display cueend     10.000000
        #       display cuedensity 0.400000
        #       display cuemode    Exp2
    }

}


user add key u {
    #makes the selections of the top molecule to auto update each frame
    set n [molinfo top get numreps]
    for {set i 0} {$i < $n} {incr i} {
        mol selupdate $i top on
    }
}


## Copy top molecule using topotools
if {[namespace exists TopoTools]} {
    user add key c {

        set mol [molinfo top]

        ## Save represenations and viewpoints
        save_rep 99999
        save_viewpoint 99999 $mol

        ## Copy the molecule
        set newmol [::TopoTools::mergemols $mol]

        restore_rep 99999 0 $newmol
        cpy_viewpoint 99999 $mol $newmol

    }
}

## Apply Viewpoint across mols
user add key C {
    set molid [molinfo top]
    save_viewpoint 99999 $molid

    foreach mol [molinfo list] {
        cpy_viewpoint 99999 $molid $mol
    }
}

## Apply representation of top mol to all mols
user add key a {
    #cpymolrep [molinfo list]
    save_rep 99999 [molinfo top]
    restore_rep 99999 0
}

user add key {;} {
    #Calls tkcon console window to the top (after it was once started from the VMD menu)
    tkcon show
}

user add key {'} {
    menu graphics on
}

user add key {[} {
    menu main on
}

    user add key {]} {
        #Preocedure sets current working folder to the path to the last loaded file of the top molecule
        lassign {*}[molinfo top get filename] psf pdb
        puts $psf
        catch {cd [file dirname $psf]}
        pwd
        menu files on
    }


user add key "\\" {
    menu sequence on
}

user add key {r} {
    mouse stoprotation
    mouse mode 0 0
}

proc write_vector { vec filename } {
    set fid [open $filename w]
    foreach elem $vec { puts $fid $elem }
    close $fid
}


proc fx { } {
    # Rotate (flip) protein 180 degrees around x axis
    set sel [atomselect top all]
    $sel move [transaxis x 180]
    $sel delete
}
proc fy { } {
    # Rotate (flip) protein 180 degrees around y axis
    set sel [atomselect top all]
    $sel move [transaxis y 180]
    $sel delete
}
proc fz { } {
    # Rotate (flip) protein 180 degrees around z axis
    set sel [atomselect top all]
    $sel move [transaxis z 180]
    $sel delete
}

# define a new, very transparent material 'Glass'
material add Glass
material change ambient   Glass 0.00
material change specular  Glass 0.50
material change diffuse   Glass 0.65
material change shininess Glass 0.53
material change opacity   Glass 0.15


# define a new, semitransparent strictly white material 'Slice', for making protein crossection pictures
material add Slice
material change ambient   Slice 1.00
material change specular  Slice 0.00
material change diffuse   Slice 1.00
material change shininess Slice 0.00
material change opacity   Slice 0.75

# define a new, non-shiny white material 'Gypsum', for making BW protein pictures
material add Gypsum
material change ambient Gypsum 0.000000
material change specular Gypsum 1.000000
material change diffuse Gypsum 1.000000
material change shininess Gypsum 0.000000
material change opacity Gypsum 1.000000

# define a new, non-shiny gray material 'Smog', for making BW protein crossections
material add Smog
material change ambient Smog 0.400000
material change specular Smog 0.000000
material change diffuse Smog 0.000000
material change shininess Smog 0.000000
material change opacity Smog 1.000000

proc vmdrestoremycolors {} {

    set colorcmds {
        {color Restype {Solvent} iceblue}
        {color Restype {Unassigned} green}
        {color Restype {Nonpolar} yellow}
    }

    foreach colcmd $colorcmds {
        set val [catch {eval $colcmd}]
    }
}


## Rotate molecule to bring bond between id1, id2 along +/- x, y, or z
proc bondto {axis sel id1 id2} {

    set idx [$sel get index]
    set xyz [$sel get {x y z}]

    set v {}
    lappend v [lindex $xyz [lsearch -exact -integer $idx $id1]]
    lappend v [lindex $xyz [lsearch -exact -integer $idx $id2]]

    #Moves COM of the molecule to the origin
    $sel moveby [vecscale -1.0 [measure center $sel weight mass]]

    ## Rotate to bring along x
    set r [vecinvert [vecsub {*}$v]]
    $sel move [transvecinv $r]

    ## Check for +/- orientation along x
    set a [vecdot $r {1 0 0}]
    if {$a < 0.0} {
        $sel move [transaxis z 180]
    }

    switch -- $axis {
        x {}
        y {$sel move [transaxis z -90 deg]}
        z {$sel move [transaxis y 90 deg]}
        -x {$sel move [transaxis z 180 deg]}
        -y {$sel move [transaxis z 90 deg]}
        -z {$sel move [transaxis y -90 deg]}
        default {puts "axis must be x, y or z"}
    }
}

# +-------------------+
# |      Axel's hacks |
# +-------------------+

if { 1 } {
    # modified to include VMD Main
    # define global variable to store X window id.
    set vmd_opengl_wid -1
    global vmd_opengl_wid
    set vmd_main_wid -1
    global vmd_main_wid

    # callback function to be called when the top molecule changes
    proc vmd_change_window_name {args} {
        global vmd_main_wid
        global vmd_opengl_wid
        if {[molinfo num] < 1} return

        if {[llength $args] == 0} {
            set name [join [molinfo top get name]]
        } else {
            set name [lindex $args 0]
            if { [string equal $name vmd_molecule] } {
                set name [join [molinfo top get name]]
            }
        }
        if {$vmd_opengl_wid > 0} {
            catch {exec xprop -id $vmd_opengl_wid \
                       -set WM_NAME "VMD: $name"}
            catch {exec xprop -id $vmd_opengl_wid \
                       -set WM_ICON_NAME $name}
        }
        if {$vmd_main_wid > 0} {
            catch {exec xprop -id $vmd_main_wid \
                       -set WM_NAME "VMD Main: $name"}
            catch {exec xprop -id $vmd_main_wid \
                       -set WM_ICON_NAME $name}
        }
    }

    # activate callback
    trace variable vmd_molecule w vmd_change_window_name

    # record window id for automatic title change
    after idle {
        global vmd_opengl_wid
        if {![catch {exec xwininfo -name \
                         "VMD [vmdinfo version] OpenGL Display"} val ]} {
            set vmd_opengl_wid [lindex $val 3]
        }
        if {![catch {exec xwininfo -name \
                         "VMD Main"} val ]} {
            set vmd_main_wid [lindex $val 3]
        }
        vmd_change_window_name
    }

}