SanDisk Membrain Software Bedienungsanleitung PDF herunterladen (Seite 11)

1 BUILDING A STRUCTURAL MODEL OF KCSA 11

5 Finally, repeat the same procedure to create segment D by typing the

following commands:

mol delete top

mol new 1K4C.pdb

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

$sel set segname D

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

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

$sel writepdb KCSA-D.pdb

$sel delete

6 Exit VMD and locate the four ﬁles named KCSA-A.pdb, KCSA-B.pdb,

KCSA-C.pdb, and KCSA-D.pdb, each one containing one segment of the

tetramer. If anything seems wrong, use the script buildtetra.tcl to

regenerate the correct ﬁles.

Now that you have created all monomers you will merge them into one single

ﬁle.

7 Use the cat command in Unix to concatenate all ﬁles by typing in a Ter-

minal window: cat KCSA-A.pdb KCSA-B.pdb KCSA-C.pdb KCSA-D.pdb

> KCSA.pdb. If you are using Windows, use a text editor to copy and

paste the contents of all ﬁles into one ﬁle called KCSA.pdb.

8 Using a text editor open the ﬁle KCSA.pdb, search for END and delete the

lines:

END

CRYST1 155.330 155.330 76.270 90.00 90.00 90.00 P 1 1

that are between segments A and B, B and C, as well as those found

between segments C and D.

Directly editing pdb ﬁles (as done above) is undesirable, you may want to cre-

ate a Tcl script that performs the same operations while preserving appropriate

indexing and formatting instead.

9 Save the modiﬁed ﬁle as KCSA-ALL.pdb. Open VMD, load KCSA-ALL.pdb,

and s et up the following representations:

Selection Drawing Method Coloring Method

protein NewCartoon SegName

not protein VDW Name

1 2 ... 6 7 8 9 10 11 12 13 14 15 16 ... 42 43

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SanDisk Membrain Software Bedienungsanleitung Seite 11