Visualization of the membrane

How to display biomolecules in motion: from rasmol to Alias Wavefront.
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m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am

Visualization of the membrane

Post by m.kalavera » Wed Mar 11, 2009 9:46 am

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

denniej0
Posts: 6
Joined: Tue Jul 01, 2008 11:11 pm

Re: Visualization of the membrane

Post by denniej0 » Wed Mar 11, 2009 7:49 pm

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!
--------------------------------------------

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"
}
}

denniej0
Posts: 6
Joined: Tue Jul 01, 2008 11:11 pm

Re: Visualization of the membrane

Post by denniej0 » Wed Mar 11, 2009 7:55 pm

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!

m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am

Re: Visualization of the membrane

Post by m.kalavera » Thu Mar 12, 2009 9:54 am

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

oliver
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Posts: 18
Joined: Fri Jun 27, 2008 8:18 pm
Location: Oxford, UK
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Re: Visualization of the membrane

Post by oliver » Tue Oct 06, 2009 3:09 pm

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.)

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