Hi Abhik,
Try this (with PyMOL 2.1 or newer):
load avg.pdb
loadall frame*.pdb
extra_fit (frame*) & guide, avg
multifilesave {name}-aligned.pdb, frame*
https://pymolwiki.org/index.php/load
https://pymolwiki.org/index.php/loadall
https://pymolwiki.org/index.php/extra_fit
https://pymolwiki.org/index.php/multifilesave
Cheers,
Thomas
> On Aug 9, 2018, at 11:32 AM, abhik.gh...@bose.res.in wrote:
>
> Hello all
> I want to align each frame pdb w.r.t a specific frame pdb. Let assume i
> have 10 pdb files.I have another file "avg.pdb". I want to align each pdb
> w.r.t "avg.pdb" file. I can do it manually using align command i.e align
> 1, avg. But is there any code or anything by which i can produce alignment
> files and save them as new pdb.
> Any suggestion is welcome
> Thank you
> Abhik
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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