Hi!
Regarding the question posted by Tamas for creating artificial
side-chains for amino acids last week:
To superimpose two (or more) residues/atoms, one needs to do a singular
value decomposition, which
gives the required rotation matrix and shift vector. The recent
biojava 1.4 release could not do this,
but after doing a little bit of research and using available open
source as template, biojava - cvs can do this now!
A "screenshot" of two superimposed residues is available at:
http://www.sanger.ac.uk/Users/ap3/rotation_example.html
This is achieved by using the Jama library which is under us. gov.
public domain license (i.e. do whatever you want).
It is located at http://math.nist.gov/javanumerics/jama/
I added the few files from this package to the biojava cvs repository
under org.biojava.structure.jama.
I thought that biojava should not have yet another .jar dependency, so
inclusion of the code is better.
There is now also a class called SVDSuperimposer. It is heavily
inspired by some code available from our friends
at Biopython.... :-) Thanks also to Peter Lackner for providing an
example for how to calculate "virtual"
CB atoms.
Now Tamas: back to your problem. I think you want to do something like
the code below:
Regards,
Andreas
try{
// get two amino acids from somewhere
String filename = "/Users/ap3/WORK/PDB/5pti.pdb" ;
PDBFileReader pdbreader = new PDBFileReader();
Structure struc = pdbreader.getStructure(filename);
Group g1 = (Group)struc.getChain(0).getGroup(56);
Group g2 = (Group)struc.getChain(0).getGroup(21);
if ( g1.getPDBName().equals("GLY")){
if ( g1 instanceof AminoAcid){
Atom cb = Calc.createVirtualCBAtom((AminoAcid)g1);
g1.addAtom(cb);
}
}
if ( g2.getPDBName().equals("GLY")){
if ( g2 instanceof AminoAcid){
Atom cb = Calc.createVirtualCBAtom((AminoAcid)g2);
g2.addAtom(cb);
}
}
System.out.println(g1);
System.out.println(g2);
// convert the Groups to Atom arrays
Atom[] atoms1 = new Atom[3];
Atom[] atoms2 = new Atom[3];
atoms1[0] = g1.getAtom("N");
atoms1[1] = g1.getAtom("CA");
atoms1[2] = g1.getAtom("CB");
atoms2[0] = g2.getAtom("N");
atoms2[1] = g2.getAtom("CA");
atoms2[2] = g2.getAtom("CB");
// and do the SVD ...
SVDSuperimposer svds = new SVDSuperimposer(atoms1,atoms2);
// the rotation matrix to be applied to group2
Matrix rotMatrix = svds.getRotation();
// and the vector to shift group2
Atom tranMatrix = svds.getTranslation();
// now we have all the info to perform the rotations ...
// clone group2 - we want to preserve the original coords
for the output later.
Group newGroup = (Group)g2.clone();
// and rotate it
Calc.rotate(newGroup,rotMatrix);
// shift the group ...
Calc.shift(newGroup,tranMatrix);
// that's it!
///
// now we finish up with doing some output:
// write to a file to view in a viewer
String outputfile = "/Users/ap3/WORK/PDB/rotated.pdb";
FileOutputStream out= new FileOutputStream(outputfile);
PrintStream p = new PrintStream( out );
// create a new structure that contains the data to be
written to the file.
Structure newstruc = new StructureImpl();
// add the group1
Chain c1 = new ChainImpl();
c1.setName("A");
c1.addGroup(g1);
newstruc.addChain(c1);
// add the now correctly positioned group2
Chain c2 = new ChainImpl();
c2.setName("B");
c2.addGroup(newGroup);
newstruc.addChain(c2);
// show where the group was originally ...
Chain c3 = new ChainImpl();
c3.setName("C");
//c3.addGroup(g1);
c3.addGroup(g2);
newstruc.addChain(c3);
p.println(newstruc.toPDB());
p.close();
System.out.println("wrote to file " + outputfile);
} catch (Exception e){
e.printStackTrace();
}
On 2 Dec 2005, at 13:02, Tamas Horvath wrote:
Thanks for the codes! I've noticed the methods in Calc, but my main
question is the following. Let's say I've got a primitive library of
AminoAcides. They stored as a group, they have all the atoms. When I'm
mutating the chain, I want to keep the backbone atoms in place, so as
far as your mutate method goes it's ok. But now I want to replace the
sidechain. In order to do that, I'd shift and rotate the desired AA in
place (Cbs would be identical and the other backbone atoms as close as
possible), and then copy the sidechain atoms to the mutated AA... (I
hope that's clear)
So do I have to wrap my Group objects to a Chain/Structure object in
order to shift and rotate them?
I don't really get how the rotation is supposed to work... what is
exactly the matrix it asks for?
-----------------------------------------------------------------------
Andreas Prlic Wellcome Trust Sanger Institute
Hinxton, Cambridge CB10 1SA, UK
+44 (0) 1223 49 6891
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