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 <llu@cs.hku.hk> 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
> gth845m@mail.gatech.edu
>
>
> Quoting Lu Lin <llu@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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