I have a program that would calculate the limits of the protein along
it's axes of inertia (besides doing many other things).
If you are interested, please let me know.
Thanks
Abhinav
j...@ssrl
Phone: (650) 926-2992
Fax: (650) 926-3292
Francois Berenger wrote:
Hello,
Is there a ccp4
Strictly speaking even Tim's solution may not give the true 'smallest
box', by which I assume is meant 'minimal volume box'. I suspect
moleman does this calculation (my apologies to Gerard if I'm wrong!)
by determining the axes of inertia, then rotating the molecule by the
matrix of eigenvectors a
Dear Francois,
I don't know if the pdbset command Clemens and Eleanor suggested actually
gives you the answer you are looking. Take for example this case:
---
| /|
|/ |
---
assume the diagonal line is the protein as it is inside the unit cell, the
unit cell dimensions are not the smallest b
Francois Berenger wrote:
Hello,
Is there a ccp4 tool to find automatically the smallest virtual
orthogonal "box" that contain a given PDB ?
Even if your favorite tool is not part of ccp4, I would be happy
to know about it. ;)
Thanks,
Francois.
pdbset xyzin thisprotein.pdb
end
This prints out
Hi,
On Wed, Mar 24, 2010 at 04:18:04PM +0900, Francois Berenger wrote:
> Hello,
>
> Is there a ccp4 tool to find automatically the smallest virtual
> orthogonal "box" that contain a given PDB ?
echo END | pdbset xyzin your.pdb xyzout /dev/null | \
awk '/Orthogonal Coordinate limits/,/On Z/'
Hi Francois,
a non-ccp4 tool:
if you have PHENIX installed then:
iotbx.pdb.box_around_molecule model.pdb
will do it (if I correctly understood you question).
You can also specify a buffer region around a molecule:
iotbx.pdb.box_around_molecule model.pdb --buffer-layer=5
Pavel.
On 3/24/10
Hello,
Is there a ccp4 tool to find automatically the smallest virtual
orthogonal "box" that contain a given PDB ?
Even if your favorite tool is not part of ccp4, I would be happy
to know about it. ;)
Thanks,
Francois.
