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Psico
| Type | Python Module |
|---|---|
| Download | https://github.com/speleo3/pymol-psico |
| Author(s) | Thomas Holder and Steffen Schmidt |
| License | BSD-2-Clause |
psico is a python module which extends PyMOL with many commands. It was developed as an in-house script collection, but grew to a quite comprehensive PyMOL extension. Some of the provided commands are already in the PyMOLWiki Script Library, but it contains also many new stuff.
Installation
Using PyMOL 2.0 from the schrodinger anaconda channel:
conda install -c schrodinger pymol conda install -c schrodinger pymol-psico
Alternatively, copy the psico folder to your PYTHONPATH or use the setup.py based installation.
Usage
To import all commands with one line:
import psico.fullinit
A reference document with all commands can be generated with:
import psico.fullinit
import psico.helping
psico.helping.write_html_ref('psico-commands.html')
Initialization
By importing psico.fullinit, the PyMOL core commands save and fetch become overloaded. In addition, all psico commands will be added to the pymol.cmd namespace. The save command will have enhanced PDB output, namely saving of secondary structure and crystal information, if available. The fetch command will also fetch 5-letter codes (code + chain) as well as CATH and SCOP identifiers (SCOP requires setting up a MySQL database). To skip the overloading, initialize psico like this:
import psico
psico.init(save=0, fetch=0, pymolapi=0)
Command List
This list might change. If you install psico, it's recommended to generate a reference document as described above to see which commands are actually available.
A "outdated" note in the table means that the code in psico is newer (somehow enhanced) than on the corresponding wiki page.
| Command | Already in PyMOLWiki... | Added to PyMOL |
|---|---|---|
| add_missing_atoms | ||
| aaindex2b | AAindex (outdated) | |
| alignwithanymethod | TMalign | |
| alphatoall | AlphaToAll (outdated) | |
| angle_between_domains | ||
| angle_between_helices | AngleBetweenHelices (outdated) | |
| apbs_surface | ||
| api_info | 1.7.2 (as api) | |
| apropos | apropos | |
| atmtypenumbers | ||
| biomolecule | BiologicalUnit/Quat (outdated) | |
| cafit_orientation | AngleBetweenHelices | |
| cbm | similar: Color Objects | |
| cbs | ||
| centerofmass | similar: center_of_mass | 1.7.2 |
| closest_keyframe | ||
| collapse_resi | similar: CollapseSel | |
| consurfdb | ||
| corina | ||
| delaunay | similar: PyDet plugin | |
| diff | ||
| dss_promotif | ||
| dssp | similar: dssp stride plugin | |
| dyndom | ||
| extra_fit | extra_fit | 1.7.2 |
| fasta | see also: Aa_codes | |
| fetch | ||
| frames2states | ||
| gdt_ts | ||
| get_keyframes | ||
| get_raw_distances | get_raw_distances | |
| get_sasa | ||
| get_sasa_ball | ||
| get_sasa_mmtk | ||
| grepset | grepset | |
| gyradius | radius of gyration (outdated) | |
| helix_orientation | AngleBetweenHelices (outdated) | |
| hydropathy2b | ||
| intra_promix | ||
| intra_theseus | ||
| intra_xfit | ||
| iterate_plot | ||
| join_states | 1.7.2 | |
| load_3d | ||
| load_aln | ||
| load_consurf | ||
| load_gro | ||
| load_msms_surface | ||
| load_mtz_cctbx | ||
| load_traj_crd | ||
| loadall | 1.7.2 | |
| local_rms | ||
| loop_orientation | AngleBetweenHelices | |
| map_new_apbs | ||
| matrix_to_ttt | ||
| mcsalign | ||
| morpheasy | ||
| morpheasy_linear | ||
| mse2met | 1.6.0 | |
| msms_surface | ||
| mutate | ||
| mutate_all | ||
| nice | ||
| normalmodes_mmtk | ||
| normalmodes_pdbmat | ||
| normalmodes_prody | ||
| paper_png | ||
| paper_settings | ||
| pca_plot | ||
| pdb2pqr | ||
| peptide_rebuild | ||
| peptide_rebuild_modeller | ||
| pir | ||
| plane_orientation | ||
| polyala | ||
| promix | ||
| prosmart | ||
| ramp_levels | ||
| remove_alt | similar: removealt | |
| rms_plot | ||
| rmsf2b | ||
| save | ||
| save_colored_fasta | ||
| save_movie_mpeg1 | ||
| save_pdb | ||
| save_settings | save_settings | |
| save_traj | save2traj (outdated) | |
| save_xyzr | ||
| sculpt_relax | ||
| select_distances | get_raw_distances | |
| select_pepseq | ||
| select_sspick | ||
| set_phipsi | ||
| set_sequence | ||
| sidechaincenters | ||
| snp_ncbi | ||
| snp_uniprot | ||
| spectrum_states | spectrum_states | |
| spectrumany | spectrumany | 1.6.0 (as spectrum) |
| split_chains | split_chains | 1.6.0 |
| split_molecules | similar: split_object | |
| sst | ||
| stride | similar: dssp stride plugin | |
| stub2ala | ||
| supercell | supercell | |
| symdiff | ||
| symexpcell | supercell | |
| theseus | ||
| tmalign | TMalign | |
| update_identifiers | ||
| xfit |