SanDisk Membrain Software Manual do Utilizador descarregar pdf (Página 22)

1 BUILDING A STRUCTURAL MODEL OF KCSA 22

Figure 6: Solvating exposed areas of a membrane protein. The left panel shows

KcsA colored by residue type. An hydrophobic be lt can be identiﬁed. The

center panel shows the outcome of raw solvation. The right panel depicts KcsA

surrounded by water at its solvent-exposed sites (leaving an appropriate space

for the membrane).

9 Now we set our selection text, and unmark the waters which it selects:

set seltext "segname SOLV and same residue as \

((z < -20) or (z>10))"

set sel [atomselect top $seltext]

$sel set beta 0

Notice how easily we can select atoms depending on their spatial location.

Other geometric selections are equally easy. Also notice the use of same

residue as: if any atom of the water molecule ﬁts our geometric criteria,

all atoms of that molecule are marked.

10 We will delete by segid and resid, since each water molecule is its own

residue. Therefore, we now make a list of these for the marked molecules:

set badwater [atomselect top "name OH2 and beta > 0"]

set seglist [$badwater get segid]

set reslist [$badwater get resid]

Since we are deleting by residue, we only want one entry per molecule

in each of these lists, and so we select all water oxygen atoms which are

marked.

11 Now we use psfgen to read the PSF and PDB ﬁles, and delete the residues

we just marked:

1 2 ... 17 18 19 20 21 22 23 24 25 26 27 ... 42 43

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