biowerkzeug

Dear HIPPO users,
I'm right now on the search for a possible visualization of the membrane for my GBIM simulations, so that I get an idea where it is in relation to my protein. My first idea was to create a grid or a block in VMD with the help of the draw command in tcl, but I am supposed there are better solutions for this problem, that look way more attractive. So if you have a visualization idea for the membrane in HIPPO, just tell me.
Hopefully waiting for your input,
M.Kalavera

The simplest ways to "view" an implicit bilayer in VMD is to use the draw commands or create a pdb file with points and then do a trace of those.

Below is a quick tcl script for the VMD to draw an implicit bilayer. If any errors occur just rename GBSWmemb to a command not used in VMD and that should fix any error problems.

Hopefully that's helpful!
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proc GBSWmemb {hydro inter {fill 0}} {
# calculate upper and lower planes
set sel [atomselect top all]
graphics [molinfo top] delete all
set scale_f 3.0
set coords [lsort -real [$sel get x]]
set minx [expr [lindex $coords 0] * $scale_f]
set maxx [expr [lindex [lsort -real -decreasing $coords] 0] * $scale_f]

set coords [lsort -real [$sel get y]]
set miny [expr [lindex $coords 0] * $scale_f]
set maxy [expr [lindex [lsort -real -decreasing $coords] 0] * $scale_f]

set h_minz [expr -1 * ($hydro/2.0 - $inter)]
set h_maxz [expr 1 * ($hydro/2.0 - $inter)]

set i_minz [expr -1 * ($hydro/2.0 + $inter)]
set i_maxz [expr 1 * ($hydro/2.0 + $inter)]

draw materials off
draw color yellow
draw line "$minx $miny $h_minz" "$minx $maxy $h_minz"
draw line "$minx $miny $h_minz" "$maxx $miny $h_minz"
draw line "$minx $maxy $h_minz" "$maxx $maxy $h_minz"
draw line "$maxx $miny $h_minz" "$maxx $maxy $h_minz"

draw line "$minx $miny $h_maxz" "$minx $maxy $h_maxz"
draw line "$minx $miny $h_maxz" "$maxx $miny $h_maxz"
draw line "$minx $maxy $h_maxz" "$maxx $maxy $h_maxz"
draw line "$maxx $miny $h_maxz" "$maxx $maxy $h_maxz"

if {$fill == 1} {
draw triangle "$minx $miny $h_minz" "$maxx $miny $h_minz" "$minx $maxy $h_minz"
draw triangle "$maxx $maxy $h_minz" "$maxx $miny $h_minz" "$minx $maxy $h_minz"

draw triangle "$minx $miny $h_maxz" "$maxx $miny $h_maxz" "$minx $maxy $h_maxz"
draw triangle "$maxx $maxy $h_maxz" "$maxx $miny $h_maxz" "$minx $maxy $h_maxz"
}

draw color blue
draw line "$minx $miny $i_minz" "$minx $maxy $i_minz"
draw line "$minx $miny $i_minz" "$maxx $miny $i_minz"
draw line "$minx $maxy $i_minz" "$maxx $maxy $i_minz"
draw line "$maxx $miny $i_minz" "$maxx $maxy $i_minz"

draw line "$minx $miny $i_maxz" "$minx $maxy $i_maxz"
draw line "$minx $miny $i_maxz" "$maxx $miny $i_maxz"
draw line "$minx $maxy $i_maxz" "$maxx $maxy $i_maxz"
draw line "$maxx $miny $i_maxz" "$maxx $maxy $i_maxz"

if {$fill == 1} {
draw triangle "$minx $miny $i_minz" "$maxx $miny $i_minz" "$minx $maxy $i_minz"
draw triangle "$maxx $maxy $i_minz" "$maxx $miny $i_minz" "$minx $maxy $i_minz"

draw triangle "$minx $miny $i_maxz" "$maxx $miny $i_maxz" "$minx $maxy $i_maxz"
draw triangle "$maxx $maxy $i_maxz" "$maxx $miny $i_maxz" "$minx $maxy $i_maxz"
}
}

To use the script, open the tcl window and do the following commands:

source GBSWmemb
GBSWmemb <tmemb value> <msw value>

the hydrophobic core value and interface value should use the same values that you'd use for GBIM or GBSW in charmm code. For example, if you had a 35 tmemb (core) value and 2.5 msw (interface) value giving your membrane a hydrophobic core thickness would be 30 Å with interface thickness of 5 Å.

Best of luck!

Dear denniej0,
your script is amazing and it works wonderful in my movie.pdb with VMD. Thanks a lot for your help.
The last question I have is referring to the tmemb value you use. You wrote that a tmemb value of 35 would produce an core of 30 Å. Why does't it produce a core with 35 Å ? This is the only point left open for me at this state and it would be great if you could answer this last lag of knowledge. I am really happy about your script and thanks bomb again.

MfG M.Kalavera

The definition of the membrane from gbsw.doc:

4. Low-dielectric slab for membrane
The influence of membrane hydrophobic core as the low dielectric
medium is approximately captured in the GBSW module (see reference 2
for details). Note that the membrane switching function is applied in
the following region;

Z > 0 : Tmemb/2.0 - MSW to Tmemb/2.0 + MSW
Z < 0 : -Tmemb/2.0 + MSW to -Tmemb/2.0 - MSW

(This is how the values TMEMB and MSW are interpreted for CHARMM; I don't think that it's exactly the same for Hippo but it should explain what denniej0 said in the original post.)