Hi,I am attaching a program that will do what you want.After entering the file names (one fixed and the other moving), the program asks for anchor atom names, i.e. a few atoms in your ligand that you want to use as reference atoms for computing the alignment. If you do not give any atom names,
Mon., April. 13th 2009
EBI
On Sun, 12 Apr 2009, rui wrote:
Hi, All
I have dozens of complex structures ( protein + ligand ) and want to align
the structures based on the ligand. Does anyone know such kind of program?
Or if can get the information around the ligand site, that would be even
Coot can do that. You can use lsq to overlap the whole atoms of ligands.
Another way is using LigAlign in Pymol.
Good luck!
leo
rui wrote:
Hi, All
I have dozens of complex structures ( protein + ligand ) and want to
align the structures based on the ligand. Does anyone know such kind
of
Hi,
To complete the responses you already have got, I recommend to use
LSQMAN ( http://xray.bmc.uu.se/usf/lsqman_man.html ) for your alignment
task. It can only compare two structures at a time but LSQMAN can easily
be run script-based (using one structure as the reference).
Select either all
Hi, All
I have dozens of complex structures ( protein + ligand ) and want to align
the structures based on the ligand. Does anyone know such kind of program?
Or if can get the information around the ligand site, that would be even
better.
Thanks.
R
If you mean that you have many structure files for the same protein but with
different ligands you can automatically align them all based on just the target
site CA atoms (i.e. defined as those close to one of the ligands) using the
Job/Cocrystal superposition application in MIFit8
Thanks for the answer. Actually, it's the opposite. I have many structures
that have different protein but with the same ligand(sugar). And I want to
fixed the ligand and align the different proteins to see the active site.
On Sun, Apr 12, 2009 at 7:36 PM, John Badger jbadg...@san.rr.com wrote:
