SanDisk Membrain Software Bedienungsanleitung PDF herunterladen (Seite 27)

2 PLACING KCSA IN A MEMBRANE 27

Grubm¨uller’s Solvate program, we want to ﬁnd good selection criteria in VMD,

and then mark the molecules we want to delete. All commands in this section

are also included in the script remove lipwat.tcl.

We will again use the beta ﬁeld of the atoms to mark the “bad lipids”. This

time, though, the selection will be slightly more complicated.

1 Enter the following commands to set beta of all atoms to zero:

mol delete all

mol new kcsa popc raw.psf

mol addfile kcsa popc raw.pdb

set POPC "resname POPC"

set all [atomselect top all]

$all set beta 0

Note that we also set a shortcut for the POPC selection resname POPC.

2 We will make three diﬀerent selections, ﬁrst marking lipids whose phospho-

rus atom lies well within the region of the KcsA, then marking remaining

lipids within a certain distance of the protein:

set seltext1 "$POPC and same residue as \

(name P1 and z>0 and abs(x)<15 and abs(y)<15)"

set seltext2 "$POPC and same residue as \

(name P1 and z<0 and abs(x)<10 and abs(y)<10)"

set seltext3 "$POPC and same residue as (within 0.6 of protein)"

set sel1 [atomselect top $seltext1]

set sel2 [atomselect top $seltext2]

set sel3 [atomselect top $seltext3]

$sel1 set beta 1

$sel2 set beta 1

$sel3 set beta 1

set badlipid [atomselect top "name P1 and beta > 0"]

set seglistlipid [$badlipid get segid]

set reslistlipid [$badlipid get resid]

We choose based on the phosphorus atom because there is only one of

them per POPC lipid.

Note that for a cylindrical protein we could have used a geometric criteria like

x ˆ 2+y ˆ 2>225, but because of the rather conical shap e of KcsA, we used two

diﬀerent selections for the two laye r of lipids. In the present example, the third

selection (seltext3) may override the previous two selections, but that may

not be the case in proteins featuring pores.

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SanDisk Membrain Software Bedienungsanleitung Seite 27