save 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, 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 save thisSession.pse
cmd.save(filename[, selection[, state[, format]]])
- When saving a session file, then "state" has no effect.
- Default is state = -1, which saves only the current state.
- When state = 0, all states in the file are written. If you have more than one state, this produces a multi-state PDB file.