From PyMOLWiki

save writes selected atoms to a file.

Details

• The file format is autodetected if the extension is ".pdb", ".pse", ".mol", ".mmod", or ".pkl".
• If the file extension ends in ".pse" (PyMOL Session), the complete PyMOL state is always saved to the file (the selection and state parameters are thus ignored).
• CLUSTALW formatted alignments can be written by PyMOL as well. Once you perform an alignment like the following,

align proteinA, proteinB, object=A_on_B

the alignment can be written using:

save A_aligned_with_B.aln, A_on_B

USAGE

save file [,(selection) [,state [,format]] ]

EXAMPLES

# save only the alpha carbons
save onlyCAs.pdb, n. CA
 
# save my MD trajectory file to disk
save myTraj.pdb, myMDTrajectory, state=0
 
# save a PyMOL session
save thisSession.pse

PYMOL API

cmd.save(file, selection, state, format)

NOTES

• When saving a session file, then "state" has no effect.
• When state = 0, all states in the file are written. If you have more than one state, this produces a multi-state PDB file.

SEE ALSO

  Load, Get Model