pymolshortcuts

This repository for pymolschortucts.py which contains 187 functions in 20 categories mapped to short-names that work like aliases (the table below is incomplete). These shortcuts include many convenience functions that make work in PyMOL more productive and fun! Some shortcuts save the many hours of work required to assemble a new script file while other shortcuts save only a few minutes but lower motivational barriers. You do not need to understand Python to be able run the script. To have the shortcuts always available, add the command 'run ~/pymolshortcuts.py' to your pymolrc or pymolrc.pml file in your home directory to load the functions in pymolshortcuts.py on startup of PyMOL. In spite of the command run, the functions will be loaded into memory but not executed. Enter SC to get a list of shortcuts printed to the command history window. Enter help PW to print the documentation for the shortcut PW to the command history window. While most shortcuts are ready to use, some shortcuts require the path names to the executables on your computer and some requrie access to Python modules that were not packaged with the incentive version of PyMOL. Use help(shortcutname) to learn how to install the required module(s).

For example, the BW command makes cartoon or sphere representations of the currently loaded molecule into black and white figures suitable for classroom handouts and coloring books for aspiring scientists.

The shortcut PW takes one or more search terms and the sends them to the PyMOL Wiki. A browser tab opens for each search term, so multiple searches are run in parallel while you continue your work in PyMOL. You can inspect the results of the searches when there is a natural break in your work in PyMOL. Other search functions can submit parallel searches of PubMed, Google, bioRxiv, Research Gate, GitHub, and more. See the tables below.

Another class of shortcuts launch your favorite full-featured text editor from within PyMOL. You have to install the text editor and edit the file path to the executable.

Another class of shortcuts opens the manuscript or grant application that you are working on in Overleaf. You have to edit the script by pasting in the appropriate link to the specific document.

Another class of shortcuts saves files with timestamps embedded in the filename to avoid overwriting png, pdb, pse, and other types of files written out from PyMOL. These save function names begin with s, (e.g., spse filename saves the current session with date and time to nearest second embedded in the file name). You can delete the unwanted version(s) at a latter time. These functions are useful if you do not have these files under version control.

The functions are stored in a single file: pymolshortcuts.py

Edit the file paths to outside executables like text editors. The shortcuts work best on the command line below the command history window because you can copy and paste text onto this command line.

Videos that demonstrate representatives from each class of shortcut are planned.

Print shortcuts and their descriptions

Shortcuts	Description
SC	Print to screen list of the shortcuts that are available in the script pymolshortcuts.py.
github	Print the url of the README file for the pymolshortcuts repository.

Show many models (NMR and crystal packing)

Shortcuts	Description
nmr	Show all of the models in nmr structure.
nmroff	Hide all but first model in a nmr structure.
rmsc	Remove supercell and the symmetry mates.
sc111	Make a lattice of 1 x 1 x 1 unit cells.
sc221	Make a lattice of 2 x 2 x 1 unit cells.
sc112	Make a lattice of 1 x 1 x 2 unit cells.
sc222	Make a lattice of 2 x 2 x 2 unit cells.
sc331	Make a lattice of 3 x 3 x 1 unit cells.
sc313	Make a lattice of 3 x 1 x 3 unit cells.
sc133	Make a lattice of 1 x 3 x 3 unit cells.
sc333	Make a lattice of 3 x 3 x 3 unit cells.

Save files with date and time in filename

Shortcuts	Description
saln	Save a aln file (alignment file) with a time stamp included in the filename to avoid overwriting work..
scif	Save a cif file (Crystallographic Information File) with a time stamp included in the filename to avoid overwriting work..
sccp4	Save a ccp4 file (CCP4 electron density map file) with a time stamp included in the filename to avoid overwriting work..
sdae	Save a dae file (Collada File) with a time stamp included in the filename to avoid overwriting work..
sdat	Save dat file (output data file) with a time stamp included in the filename to avoid overwriting work.
sfasta	Save a fasta file (sequence file) with a time stamp included in the filename to avoid overwriting work..
sidtf	Save a idtf file (Intermediate Data Text Format) with a time stamp included in the filename to avoid overwriting work..
smae	Save mae file (Maestro file) with a time stamp included in the filename to avoid overwriting work.
smmd	Save mmd file (Macromodel file) with a time stamp included in the filename to avoid overwriting work.
smmod	Save mmd file (Macromodel file) with a time stamp included in the filename to avoid overwriting work.
spmo	Save pmo file (XYZ, binary format file) with a time stamp included in the filename to avoid overwriting work.
smoe	Save moe file (Molecular Operating Environment) with a time stamp included in the filename to avoid overwriting work.
smol	Save mol file with a time stamp included in the filename to avoid overwriting work.
smol2	Save mol2 (Sybyl file format) file with a time stamp included in the filename to avoid overwriting work.
smtl	Save mtl (Wavefront Material file format) file with a time stamp included in the filename to avoid overwriting work.
sobj	Save obj file (Wavefront mesh file) with a time stamp included in the filename to avoid overwriting work.
sout	Save out file (output data file) with a time stamp included in the filename to avoid overwriting work.
spdb	Save pdb file with a time stamp included in the filename to avoid overwriting work..
spkl	Save a pkl file (Python pickle file) with a time stamp included in the filename to avoid overwriting work..
spkla	Save a pkla file (Python pickle file) with a time stamp included in the filename to avoid overwriting work..
spng	Save png file with a time stamp included in the filename to avoid overwriting work.
spov	Save pov (POV-ray tracing file format) file with a time stamp included in the filename to avoid overwriting work.
spqr	Save pqr file with a time stamp included in the filename to avoid overwriting work.
spse	Read as a commandline argument, a string as the filename stem or
ssdf	Save sdf file with a time stamp included in the filename to avoid overwriting work.
swrl	Save wrl (VRML 2 file format) file with a time stamp included in the filename to avoid overwriting work.

Make molecular representations that are not available in PyMOL

Shortcuts	Description
AO	Commands to make ambient occlusion image like those in Qutemole.
AOD	Make ambient occlusion image of any with dark carbon atoms.
BW	Commands to make black-and white-ribbon cartoon on a white background.
BU	Commands to make biological unit. Requires a pdb file. There are
CB	Loads Jared Sampson's script "colorblindfriendly.py" from the
CR	Commands to make colored filled-ring cartoon of nucleic acids. May
CSS	Commands to color ribbon or cartoon representations of proteins by
CBSS	Apply colorblind-friendly coloring to ribbon or cartoon representations.
DU	Make dumbbell (ribbons with rolled edges) cartoon of the main chains of nucleic acids and proteins.
FR	Make filled-ring cartoon of nucleic acids. May need to enter 'hide everything' first.
HH	Hide hydrogen atoms of currently visible molecular objects.
PE	Apply pearl effect about cations. Must supply selection.
PU	Make putty cartoon of main chain of nucleic acids and proteins.
SE	Commands to make SAXS envelope from a bead model.
getchem	Create selections based on the biophysical properties of each residue.
timcolor	Use Tim Mather's coloring scheme applied to the selections defined in getchem().

Launch a full-featured text editor from PyMOL

Shortcuts	Description
atom	Open file with the text editor Atom from within PyMOL.
bbedit	Open file with the text editor bbedit from within PyMOL.
code	Open file with Visual Studio Code from within PyMOL.
emacs	Open file with emacs from within PyMOL.
gedit	Open file with gedit from within PyMOL.
jedit	Open file with jedit from within PyMOL.
mate	Open file with Textmate (Mac OS only) from within PyMOL.
notepadpp	Open file with notepadpp (Mac OS only) from within PyMOL.
nv	Open file with neovim from within PyMOL.
oni	Open the editor Oni from within PyMOL.
pdbed	Open PDBEditor.jar from within PyMOL.
st3	Open sublime text 3 from within PyMOL.
vim	Open vim from within PyMOL.

Open word processord

Shortcuts	Description
word	Open word from within PyMOL.

Open data analysis programs

Shortcuts	Description
cranR	Open the Cran R from within PyMOL.
ddb	Open the DBBrowserSQLite.
excel	Open the excel from within PyMOL.
JASP	Open the JASP from within PyMOL.
JMP	Open the JMP from within PyMOL.
jabref	Open the jabref from within PyMOL.
julia	Open the jabref from within PyMOL.
oc	Open the jabref from within PyMOL.
ppt	Open the powerpoint from within PyMOL.

Open terminal windows

Shortcuts	Description
iterm	Open iTerm2 window on MacOS.
term	Open a Terminal window on MacOS.

Open other molecular graphics programs

Shortcuts	Description
ccp4mg	Open ccp4mg from within PyMOL.
chimera	Open Chimera from within PyMOL.
coot	Open coot from within PyMOL.
jmol	Open Jmol from within PyMOL.
vmd	Open vmd from within PyMOL.
yasara	Open the molecular graphics prograom YASASRA from within PyMOL.

Image manipulation programs

Shortcuts	Description
gimp	Open the molecular graphics program with gimp from within PyMOL.
inkscape	Open the molecular graphics program with gimp from within PyMOL.

Open certain webapps

Shortcuts	Description
gcal	Open Google Calendar.
GM	Open gmail.
WM	Open Web Mail in defualt browser. Adjust url for your institution.
WS	Open National Weather Service website for locale.

Samples

Shortcuts	Description
GGT	WT human gamma glutamyl transpeptidase at 1.67 Angstrom
GU	10-mer dsRNA with 8 contiguous Us. U-helix RNA.
N9	Influenza N9 neuraminidase at 1.55 Angstrom resolution, PDB code 4dgr.
T4L	WT T4 lysozyme as ribbon diagram (1.08 Ang): 3FA0.
U8	16-mer dsRNA with 8 contiguous Us. U-helix RNA (1.37 Ang): 3nd3.
WC8	16-mer dsRNA, Watson-Crick helix RNA. 1.55 Angstrom

Commands to display complex scenes.

Shortcuts	Description
BST	G2G3/U9U8 base step , PDB code 4PCO.
LG	Nine sugar glycan in influenza N9 neuraminidase at
NA	Hydrated sodium cation bound in major groove of a

Commands to display complex scenes with pdb files on computer.

Shortcuts	Description
LGGT	WT human gamma glutamyl transpeptidase at 1.67 Angstrom
LGU	10-mer dsRNA.
LN9	Influenza N9 neuraminidase at 1.55 Angstrom resolution, PDB code
LT4L	Display WT T4 lysozyme as ribbon diagram (resoluton 1.08 Ang): 3FA0.
LU8	16-mer dsRNA with 8 contiguous Us. U-helix RNA (1.37 Ang): 3nd3.
LWC8	16-mer dsRNA, Watson-Crick helix RNA. 1.55 Angstrom
LBST	G2G3/U9U8 base step , PDB code 4PCO.
LLG	Nine sugar glycan in influenza N9 neuraminidase at
LNA	Hydrated sodium cation bound in major groove of a

Re-orient molecule

Shortcuts	Description
oy	Align long axis of molecule along z-axis.
omxy	Align long axis of molecule along minus x-y axis.
oxy	Align long axis of molecule along x-y axis.
oz	Align long axis of molecule along y-axis.

Horizontal scripting

Shortcuts	Description
cntfiles	Count number of files in current directory.
cntpdb	Count number of pdb files in current directory.
rline	Enter "help(rline)" to refresh memory of the readline commands.
rv	Get the view settings in a compact format on one line.

Print commands for using git for version control

Shortcuts	Description
gitAdd	Enter help(gitAdd) to print steps for adding a file to version control.
gitCommit	Enter help(gitInit) to print steps for saving updates to a file under version control.
gitInit	Enter help(gitInit) to print steps for creating a git repository.
gitPull	Enter help(gitPush) to print steps to send to updates to a repository on github.com.
gitPush	Enter help(gitPush) to print steps to send to updates to a repository on github.com.

Send search term(s) to websites with search boxes.

Shortcuts	Description
AB	Send search term or phrase to Amazon.com Books in default browser.
def	# Send search term or phrase to anaconda.com books in default browser.
GB	Send search term or phrase to Amazon.com in default browser.
GH	Send search term or phrase to GitHub in default browser.
GHN	Send search term or phrase to GitHub in default browser.
GO	Send search term or phrase Google in default browser.
GON	Send search term or phrase Google in default browser and opens the top N results in N new tabs.
GS	Send search term or phrase to Google Scholar in default browser.
GSN	Send search term or phrase to Google Scholar in default browser.
GV	Send search term or phrase to Google Videos in default browser.
GVN	Send search term or phrase to Google Videos in default browser.
MA	Send search term to all searchable websites in pymolshortcuts:
MB	Send search term to search multiple sites for term in books:
MC	Send search term to search ten core websites in pymolshortcuts:
MM	Send search term to search for manuscripts in pymolshortcuts:
PDB	Submit a search term to the Protein Data Bank.
PDBN	Submit a search term to the Protein Data Bank and open the top N hits in separate tabs.
PML	Submit a search term to the PyMOL Users Mail Service.
PMLN	Submit a search term to the PyMOL Users Mail Service.
PM	Send search term or phrase to PubMed.
PMN	Send search term or phrase to PubMed and open top N hits in separate tabs.
IPM	Read list of search terms and submit each term to PubMed in a separate browser tab.
IPMN	Read list of search terms and submit each term to PubMed in a separate browser tab.
RG	Submit a search query of Research Gate.
RGN	Submit a search query of Research Gate and open the top N hits in sepearte tabs.
SD	Submit a search term to Science Direct.
SDN	Submit a search term to Science Direct and open the top N hits in sepearte tabs.
SF	Send search term to sourceforge.
SFN	Send search term to sourceforge and open the top N hits in sepearte tabs.
SP	Submit a search term to Springer Books
SPN	Submit a search term to Springer Books and open the top N hits in sepearte tabs.

Open static web sites

Shortcuts	Description
ACA	Open the American Crystallographic Association Annual Meeting webpage.
ALS	Open website of the Advanced Light Source.
APS	Open website of the Advanced Photon Source.
AX	Send search term or phrase to arXiv.
BC	Open the webpage of the BIOCAT biological SAXS beamline at the Advanced Photon Source.
BD	Open the webpage of the Small Angle Scattering Biological Data Bank (SASBDB).
BX	Send search term or phrase to bioRxiv
CH	Open the webste of UCSF Chimera.
CHESS	Open the website of CHESS.
EMDB	Open the website of the Electron Microscopy Data Bank.
EP	EasyPyMOL github site.
JM	Open the Jmol wiki.
IUCR	Open website of the IUCr Journals.
LBSF	Open website of Laboratory of Biomolecular Structure and Function, the X-ray diffraction core facility at OUHSC.
MCL	Open website of Macromolecular Crystallography Laboratory at the University of Oklahoma.
MG	Open website of the OUHSC molecular graphics course.
NDB	Open website of the Nucleic Acid Database.
notPyMOL	Open website with list of other molecular graphics programs.
NSLSII	Open the website of the National Synchrotron Light Source II (NSLSII) at Brookhaven National Laboratory.
PPC	Open the website of the Protein Production Facility at the University of Oklahoma in Norman.
PS	Open the home page of the Protein Soceity.
PW	Submit search of the PyMOL Wiki.
RS	Open the homepage of the RNA Society.
SAXS	Open the webpage of SAXS links at OUHSC.
SB	Open the webpage of SSRL Biological SAXS at BL 4-2.
SBGRID	Open the webpage of the Structural Biology Grid (SBGRID) YouTube Channel.
SciPy18	Open the SciPy 2018 YouTube Channel.
SSRL	Open the webpage of SSRL Structural Molecular Biology.
SSURF	Open the webpage of the Society for Science at User Research Facilities (SSURF).
SO	Submit a search term to Stackoverflow.

3D-PDFs

Shortcuts	Description
ms2pdf	Send molecular surface or ribbon cartoon from PyMOL to 3dpdf.
topdf	Send stick models as pse file from PyMOL through Jmol to 3DPDF.