VMD-L Mailing List

From: Tyler Westland (tylerofthewest_at_gmail.com)
Date: Tue Sep 20 2016 - 15:45:15 CDT

*Solved*

Solution:
Change colors of beads after they have been loaded.

Code created from suggestion:
# Run after beads have been loaded
# Change as nessecary
proc ::set_colors {} {
    # add items to color categories
    # The type is set to the color.
      # B = Blue
      # U = Blue
      # Y = Yellow
 # W = Yellow
      # R = Red
      # A = Gray
      # O = Orange
      # G = Green
    # Water and Hexane project
    # Water
    set hexanewater [atomselect top "name H or name O or name M"]
    $hexanewater set name B
$hexanewater set type B
    # Hexane
    set hexane [atomselect top "name CH2 or name CH3"]
    $hexane set name Y
    $hexane set type Y

    # SDK project
    # Water
set sdkwater [atomselect top "name W"]
$sdkwater set name U
$sdkwater set type U
    # Surfactant S10E3
    set OA [atomselect top "name OA"]
$OA set name R
$OA set type R
set EO [atomselect top "name EO"]
$EO set name W
    $EO set type W
    set CM [atomselect top "name CM"]
$CM set name G
    $CM set type G
set CT [atomselect top "name CT"]
$CT set name A
    $CT set type A
set EB [atomselect top "name EST1 or name CT2"]
$EB set name O
    $EB set type O

    # now we can define colors by color group!
if {[$hexanewater num] > 0} {
color Name B blue
color Type B blue
}
if {[$sdkwater num] > 0} {
color Name U blue
color Type U blue
}
if {[$hexane num] > 0} {
color Name Y yellow
    color Type Y yellow
}
if {[$EO num] > 0} {
color Name W yellow
    color Type W yellow
}
if {[$OA num] > 0} {
color Name R red
    color Type R red
}
if {[$CM num] > 0} {
color Name G green
    color Type G green
}
if {[$CT num] > 0} {
color Name A gray
    color Type A gray
}
if {[$EB num] > 0} {
color Name O orange
    color Type O orange
}
}

On Thu, Sep 8, 2016 at 10:17 AM, Tyler Westland <tylerofthewest_at_gmail.com>
wrote:

> Dear VMD users,
>
> VMD Version: 1.9.2
>
> Problem: Error in custom vmdrc script
>
> Problem script:
> # Our colors set by name.
> # The "after idle" command is because the .vmdrc is processed too early
> # for colors to be set; this makes it so that it occurs after other
> # stuff is properly set up.
> # The dummy molecule is created because we can't set colors if no
> # molecules exist.
> # See https://sites.google.com/site/akohlmey/random-hacks/vmd-
> initialization-scripts
> after idle {
> # create dummy molecule with one atom
> set mol [mol new atoms 20]
> set sel [atomselect $mol all]
> # add items to color categories
> # Water and Hexane project
> # Water
> $sel set name H
> $sel set type H
> color Name H blue
> color Type H blue
> $sel set name O
> $sel set type O
> color Name O blue
> color Type O blue
> $sel set type M
> $sel set name M
> color Name M blue
> color Type M blue
> # Hexane
> $sel set name CH2
> $sel set type CH2
> color Name CH2 yellow
> color Type CH2 yellow
> $sel set name CH3
> $sel set type CH3
> color Name CH3 yellow
> color Type CH3 yellow
>
> # SDK project
> # Water
> $sel set name W
> $sel set type W
> color Name W blue
> color Type W blue
> # Surfactant S10E3
> $sel set name OA
> $sel set type OA
> color Name OA red
> color Type OA red
> $sel set type EO
> $sel set name EO
> color Name EO yellow
> color Type EO yellow
> $sel set name CM
> $sel set type CM
> color Name CM green
> color Type CM green
> $sel set name CT
> $sel set type CT
> color Name CT gray
> color Type CT gray
> $sel set name EST1
> $sel set type EST1
> color Name EST1 orange
> color Type EST1 orange
> $sel set name CT2
> $sel set type CT2
> color Name CT2 orange
> color Type CT2 orange
>
> # clean up
> $sel delete
> mol delete $mol
> }
>
> Error:
> When VMD starts up it throws an application error with this message:
>
> Unable to change color name
> Unable to change color name
> while executing
> "color Name "CH2" yellow"
> ("after" script)
>
> Thank you very much,
> Tyler Westland
>