SanDisk Membrain Software Bedienungsanleitung PDF herunterladen (Seite 9)

1 BUILDING A STRUCTURAL MODEL OF KCSA 9

REMARK 350 BIOMOLECULE: 1

REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C

REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000

REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000

REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 310.66000

REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 310.66000

REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000

REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 310.66000

REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000

REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000

REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000

REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 310.66000

REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000

5 Look at the lines labeled BIOMTn where n is a number. Each set of three

BIOMTn lines describ e s the rotations and translations necessary to generate

each subunit (notice that the ﬁrst matrix is simply a unit matrix, corre-

sponding to no transformation.) In the next section, you will see how to

use these matrices to generate the complete tetramer.

6 Now scroll down a bit more, and look at the REMARK 465 and REMARK 470

lines. These lines describe residues and atoms missing from the structure,

respectively. All structures are missing some atoms and residues and it

is important to check whether missing parts are relevant for the question

being addressed with the simulations. Below you will see how psfgen is

able to guess the co ordinates of some of the missing atoms.

7 Close the text editor.

1.3 Building the KcsA Tetramer

As you discover yourself, the PDB ﬁle 1K4C.pdb contains only one subunit of

the KcsA tetramer. However, for most proteins, there is only one subunit, or

all subunits are present in the original PDB ﬁle. Here you will build the whole

KcsA tetramer, noting that for many other membrane proteins, this step will

not be necessary.

1 Start a new VMD session and select the Extensions → Tk Console menu

item in the VMD Main window. The next four steps are also replicated

in the script buildtetra.tcl.

2 Create and save segment A of the protein by typing the following com-

mands in the Tk Console window.

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SanDisk Membrain Software Bedienungsanleitung Seite 9