Hi Hally,
Thank you for your reply! Could you tell me how to save the alignment
result to a new .pdb file?
Thanks again!
Best,
Linda
Hally Shaffer wrote:
Linda,
To align two proteins, they have to have the same number of atoms. You can
manipulate the pdb files to delete part of one protein or remove a small
molecule ligand if need be. You will need to save the "corrected" pdb files to
load for the alignment.
Attached is a picture of two proteins I aligned (one is in the apo form and the
other is the ligand-bound holo form of the protein). The major difference
between the two is indicated in red. I had to load my two pdb files and then the
ligand (rea) as a separate pdb file. The commands are below.
load 1LBDm.pdb, 1LBD
load 1FBYm.pdb, 1FBY
load REA.pdb, rea
align 1LBD, 1FBY
Good luck,
Hally
--
Hally Shaffer
<>< Graduate Student
Georgia Institute of Technology
School of Chemistry and Biochemistry
gth8...@mail.gatech.edu
Quoting Lu Lin <l...@cs.hku.hk>:
Hi all,
Anyone know which algorithm PyMOL uses to align or super of two structures?
Thanks a lot!
Best,
Linda
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