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writes selected atoms to a file.
- The file format is autodetected if the extension is .pdb, .pqr, .mol, .sdf, .pkl, .pkla, .mmd, .out, .dat, .mmod, .pmo, .pov, .png, .pse, .psw, .aln, .fasta, .obj, .mtl, .wrl, .idtf, .dae, or .mol2.
- If the file extension is ".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
save file [,(selection) [,state [,format]] ]
# 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
A Random PyMOL-generated Cover. See Covers