Re: [PyMOL] algorithm for alignment

[Lu L. <ll...@cs...>]

Hi, Abhi,
You mean save them separately? Is there some way to save them into one 
file? Thanks!!
Best,
Linda

Abhinav Verma wrote:
> there is something on the menu, file->save->molecule
> after the alignment, choose the molecule you want to save and just 
> save. pymol saves the pdb with new coordinates.
>
> cheers,
> Abhi
>
> On Jan 25, 2008 10:29 PM, Lu Lin <ll...@cs... 
> <mailto:ll...@cs...>> wrote:
>
>     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
>     > gt...@ma... <mailto:gt...@ma...>
>     >
>     >
>     > Quoting Lu Lin <ll...@cs... <mailto:ll...@cs...>>:
>     >
>     >
>     >> Hi all,
>     >>
>     >> Anyone know which algorithm PyMOL uses to align or super of two
>     structures?
>     >>
>     >> Thanks a lot!
>     >>
>     >> Best,
>     >> Linda
>     >>
>     >>
>     >>
>     >>
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