Just to be more clear:I store the AminoAcides as HashMap where 1
group contains 1AA, and the String is the name of the AA. (I prefer 1 letter
code there)
To shift the desired AA in place, I'd match the Cb atomsThen rotate the AA so
that the Ca-Cb line would matchThen rotate the AA so that the N-
Thanks for the codes! I've noticed the methods in Calc, but my main questionis
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 thechain, I want
to keep the backbone atoms in place, so as far as your mutatemet
Hi Tamas!
If I've got a Group , which is an amino acid, and I want to shift it
by a 3D vector (or 3 2D vectors), how may I do it?
There is the org.biojava.bio.structure.Calc class that allows to do
calculations with the structure.
e.g. to shift a structure do:
double x =
If I've got a Group , which is an amino acid, and I want to shift it by a
3Dvector (or 3 2D vectors), how may I do it?Similarly, if i want to rotate the
same structure, how may I do it?If you just can show me a very short sample
code, I'd really appreciate it!Thanks!
On 12/1/05, Tamas Horvath <[
Exactly... I want to keep a backbone and replace the whole sidechain
asnecessary... I know this should be relatively easy, but I'm a bit lost intthe
documentation...
On 12/1/05, Andreas Prlic <[EMAIL PROTECTED]> wrote:>> Hi Tamas,>> it is
possible to access the content of a structure and> chan
Hi Tamas,
it is possible to access the content of a structure and
change/add/drop groups and atoms as you wish.
When talking about introducing "point mutations" I assume you want to
re-label a residue's main chain
atoms and drop the side chain atoms, but keep the Cb one? this would
take
.
-
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> Tamas Horvath
> Sent: Thursday, December 01, 2005 12:21 AM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] modify structure
>
>
> Is there any way to modify a protein
Is there any way to modify a protein structure by modifying the contents ofthe
Structure object?In short, I have a Structure object, parsed from a pdb file,
and I want tointroduce point mutations to it, and save the modified structure
to a pdbfile for further analysis... (I intend to use gromacs
