1 BUILDING A STRUCTURAL MODEL OF KCSA 21
5 Enter the following commands in the Tk Console window:
mol new kcsav solv raw.psf
mol addfile kcsav solv raw.pdb
set all [atomselect top all]
$all moveby [vecinvert [measure center $all]]
display resetview
The measure center command finds the geometric center of the selection
you give it. It can also find a weighted center, such as center of mass,
center of charge, etc. The result of the command is a vector, which we
invert using the vecinvert command, and this is in turn passed to the
moveby option of the selection. Finally, we reset the view so we can see
the centered molecule again.
6 In VMD, create the following graphical representations:
Selection Drawing Method Coloring Method
protein VDW ResType
water Lines ColorID 0
water and z<-20 Lines ColorID 1
water and z>10 Lines ColorID 1
Protein residues are now colored based on their hydrophobicity and acidity.
Charged residues are colored blue and red, green residues are hydrophilic, and
white residues are hydrophobic. The hydrophobic part of the protein will be
interacting with the membrane. Can you guess then the location of the mem-
brane? We will eliminate water molecules located in the hydrophobic region of
the protein (Fig. 6).
7 Change the representation involving water molecules so as to cover differ-
ent regions along the z-axis. Is the original selection of water molecules
reasonable? Does it leave space for the membrane?
8 Now we will “mark” the water we don’t want to keep. For this, we will use
the Beta field, marking “bad water” with a beta value of 1. Since most of
the water will be deleted, we will mark all Solvate water, then change the
ones we want to keep. Type in the Tk Console window:
set solv [atomselect top "segname SOLV"]
$solv set beta 1
The PDB B-factor field. The “B” field of a PDB file typically
stores the “temperature factor” for a crystal structure and is read
into VMD’s “Beta” field. Since we are not currently interested in
this information, we can recycle this field to store our own numerical
values and use them for different purposes.
(30 paginas)
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