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 <l...@cs.hku.hk
<mailto:l...@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
> gth8...@mail.gatech.edu <mailto:gth8...@mail.gatech.edu>
>
>
> Quoting Lu Lin <l...@cs.hku.hk <mailto: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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