Hi Justin,
The program DeepView http://www.expasy.ch/spdbv/ is a very good way
to align similar structures. It is free, and there is a tutorial for
it that will tell you just what to do:
http://www.usm.maine.edu/~rhodes/SPVTut/index.html
While you will probably need to invest some time (probably 30 min or
so) in the first few sections of the tutorial so you learn how to use
DeepView, the structural alignment (see section 11 of the tutorial)
itself takes seconds in DeepView. Then you save the *project* as a
pdb file (under File Save As..).
Overall, you'll likely save time versus trying to align the
structures by hand, especially if you will need to align structures
in the future.
HTH,
Frieda
///////////////////////////////////////////
Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
///////////////////////////////////////////
On Jan 10, 2008, at 5:22 PM, Justin JEONG wrote:
Hello everyone!
I now am trying to display 3 proteins in a figures.
For example, I have 3 proteins, 1XBL.pdb, 1DKG.pdb, and 1DKX.pdb.
What I want to do is I want to display this 3 protein structures at
same time, and some residues are combinded together such that for
1XBL there are 5 interface residues of which the residue IDs are 30
36 69 71 741, for 1DKG there are 3 interface residues of which the
residue IDs are 13 116 174, and for 1DKX there are 4 interface
residues of which the residue IDs are 6 405 447 483. Based on this
information I want to put all three proteins are closed to each other.
I tried to use the commend: load append "1XBL.pdb" "1DKG.pdb"
"1DKX.pdb", but I cannot move all the proteins independently.
Do you have any idea how to handle this problem? If so, please help
me!!
Simpler example is shown below
If the structure of Protein A and B looks like this
Protein A:
|-----------|
Protein B:
___|____
|
So, what I want to do is to combine Protein A and Protein B. Just
like this.
Combine A and B
|-----------|
___|____
|
Thanks
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