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1 BUILDING A STRUCTURAL MODEL OF KCSA 10

cd "< your home directory >/mem-tutorial-files/01-BUILD/"

mol new 1K4C.pdb

set all [atomselect top all]

$all set segname A

$all writepdb KCSA-A.pdb

$all delete

Note that you should always delete selections once you are ﬁnished with

them.

Rotations and Translations in VMD. The transformation matrices

provided in REMARK 350 of a PDB ﬁle (lines labeled BIOMT) contain

4 columns and 3 rows each. The matrix formed by the ﬁrst three

columns and three rows describes a rotation, while the last column

describ e a translation. VMD uses 4×4 matrices to perform rotations

and translations, so one must add a fourth row ({0 0 0 1}) to the

matrices provided in the PDB ﬁle.

Now you will transform the coordinates of s egme nt A into those of segment B,

C, and D by using the appropriate matrix transformations as described below.

Note that we will not replicate potassium ions since they are located in the

symmetry axis of the protein.

3 Create and save segment B of the protein by typing the following com-

mands in the Tk Console window.

set sel [atomselect top "all and not name K"]

$sel set segname B

$sel move {{-1.0 0.0 0.0 310.66} {0.0 -1.0 0.0 310.66}

{0.0 0.0 1.0 0.0} {0.0 0.0 0.0 1.0}}

$sel writepdb KCSA-B.pdb

$sel delete

Note that in the previous step we used the second matrix (BIOMT2) of REMARK

350 in 1K4C.pdb with an additional row. Be sure to add spaces between vectors

delimited by {}.

4 Delete the current molecule, load the KcsA crystal structure again and

create segment C of the protein by typing the following commands in the

Tk Console window.

mol delete top

mol new 1K4C.pdb

set sel [atomselect top "all and not name K"]

$sel set segname C

$sel move {{0.0 -1.0 0.0 310.66} {1.0 0.0 0.0 0.0}

{0.0 0.0 1.0 0.0} {0.0 0.0 0.0 1.0}}

$sel writepdb KCSA-C.pdb

$sel delete

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SanDisk Membrain Software Manual do Utilizador Página 10