Difference between revisions of "Save"
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Jaredsampson (talk | contribs) (→Details: updated list of auto-detected formats [from modules/pymol/exporting.py]; added default state = -1) |
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=Details= | =Details= | ||
| − | * The file format is autodetected if the extension is | + | * 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 | + | * 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, | * CLUSTALW formatted alignments can be written by PyMOL as well. Once you perform an alignment like the following, | ||
::<source lang="python"> | ::<source lang="python"> | ||
| − | + | align proteinA, proteinB, object=A_on_B | |
</source> | </source> | ||
::the alignment can be written using: | ::the alignment can be written using: | ||
| Line 32: | Line 32: | ||
===PYMOL API=== | ===PYMOL API=== | ||
<source lang="python"> | <source lang="python"> | ||
| − | cmd.save( | + | cmd.save(filename[, selection[, state[, format]]]) |
</source> | </source> | ||
===NOTES=== | ===NOTES=== | ||
* When saving a session file, then "state" has no effect. | * 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. | * When state = 0, all states in the file are written. If you have more than one state, this produces a multi-state PDB file. | ||
Revision as of 10:54, 21 November 2013
save writes selected atoms to a file.
Details
- 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
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(filename[, selection[, state[, format]]])
NOTES
- 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.
SEE ALSO
Load, Get Model