Coot command reference

The commands below are typed into the Command tab of the Python/AI terminal. Text is matched case-insensitively and extra whitespace is ignored. Where a command takes a model or map number, omitting it acts on the active molecule.

This file is generated from the command definitions (python/coot_commands/). Do not edit by hand - run python3 -m coot_commands.docs to regenerate.

Building

add solvent SO4 here

Add a monomer (by 3-letter code) at the screen centre.

Examples:

  • add solvent SO4 here
  • add ligand GOL

Fetches the named monomer from the dictionary and moves it to the screen centre. Use “add water” for a single water atom.

add water here

Add a water at the screen centre.

Examples:

  • add water here
  • add water

Places a water atom at the screen centre (the pointer position), like the ‘Place Atom At Pointer’ tool.

Delete

delete all

Ask to confirm closing every loaded map and model.

Examples:

  • delete all
  • close everything

Asks for confirmation before closing every loaded map and model. Type ‘delete all confirm’ to go ahead.

delete all confirm

Close every loaded map and model (confirmed).

Confirms and carries out ‘delete all’, closing every loaded map and model.

delete map 1

Delete (close) a map.

Examples:

  • delete map 1
  • close map 1

Closes the given map, freeing its molecule number.

delete model 0

Delete (close) a model.

Examples:

  • delete model 0
  • close model 0

Closes the given model, freeing its molecule number.

delete molecule 2

Delete (close) a molecule of either kind.

Examples:

  • delete molecule 2
  • close mol 2

Closes the given molecule (map or model) by number.

Display

show only active

Show only the active model, hiding the others.

Hides every model except the active one.

hide residue environment

Hide the residue environment distances.

Examples:

  • hide residue environment
  • hide environment

Hides the residue environment distances.

hide map 1

Hide (undisplay) a map.

Examples:

  • hide map 1
  • undisplay map

With no map number, acts on the active map.

hide model 0

Hide (undisplay) a model.

Examples:

  • hide model 0
  • undisplay model

With no model number, acts on the active model.

show residue environment

Show the environment distances around a residue.

Examples:

  • show residue environment
  • show environment A/89

Shows the environment distances (contacts and H-bonds) around a residue, centring on it. With no residue named, uses the active residue (the one at the centre of the screen).

show map 1

Show (display) a map.

Examples:

  • show map 1
  • display map

With no map number, acts on the active map.

show model 0

Show (display) a model.

Examples:

  • show model 0
  • display model

With no model number, acts on the active model.

Fetch

fetch 3GP

Fetch a monomer from the CCD dictionary.

Examples:

  • fetch 3GP
  • fetch monomer ATP

Fetches a monomer (by 3-letter code) from the CCD dictionary. Four-or-more character codes are treated as PDB accessions.

fetch 1abc

Fetch coordinates from the PDBe.

Examples:

  • fetch 1abc
  • fetch pdb 4hhb

Fetches coordinates from the PDBe. Add “and map” to also fetch maps, or “from pdb-redo” for the re-refined version.

fetch 1abc and map

Fetch coordinates and maps (via EDS).

Examples:

  • fetch 1abc and map
  • fetch map for 1abc

Fetches coordinates and the 2Fo-Fc / Fo-Fc maps from the Electron Density Server (EDS).

fetch 1abc from pdb-redo

Fetch a re-refined model and maps from PDB-REDO.

Examples:

  • fetch 1abc from pdb-redo
  • fetch pdb-redo 1abc

Fetches the re-refined model and maps from PDB-REDO.

Help

help

List the available commands, grouped by category.

Labels

clear labels

Remove all atom labels.

Examples:

  • clear labels
  • remove all labels

Ligand

fit ligand LIG

Fit a ligand into density by its three-letter code.

Examples:

  • fit ligand LIG
  • fit ligand ATP here
  • find ligand NAG into model 0 map 1

Fits a ligand (by three-letter code) into density, the same as Ligand > Find Ligands. Uses the active model and the refinement map by default. Add ‘here’ to search only at the current view centre - handy after ‘go to blob N’. Returns the molecule numbers of the fitted solutions.

Maps

colour map 1 blue

Set a map’s colour.

Examples:

  • colour map 1 blue
  • colour map cyan

With no map number, acts on the active map.

contour map 1 to 0.35

Set a map’s absolute contour level.

Examples:

  • contour map 1 to 0.35
  • contour to 0.3

Sets the absolute contour level (map units). With no map number, acts on the active map. Add “sigma” to contour in RMSD units instead.

contour map 1 to 1.5 sigma

Set a map’s contour level in sigma.

Examples:

  • contour map 1 to 1.5 sigma
  • contour to 1.2 rmsd

Sets the contour level in sigma (map RMSD units). With no map number, acts on the active map.

map 1 is a difference map

Mark a map as a difference map.

Examples:

  • map 1 is a difference map
  • make map 2 a difference map

Marks the map as a difference map (green/red, contoured either side of zero). With no map number, acts on the active map.

Model editing

add altconf A/72

Add an alternate conformation to a residue.

Examples:

  • add altconf A/72
  • add alt conf A 72
  • add altconf

Adds an alternate conformer to the named residue. With no residue named, acts on the active residue (the one at the centre of the screen).

add OXT to A/89

Add a terminal OXT atom to a residue.

Examples:

  • add OXT to A/89
  • add OXT to A 89
  • add OXT

Adds a terminal OXT oxygen to a residue (usually a chain’s C-terminus). With no residue named, acts on the active residue (the one at the centre of the screen); with no model number, the active model.

add terminal residue to A/89

Add a terminal residue onto the end of a chain.

Examples:

  • add terminal residue to A/89
  • add terminal residue
  • add terminal residue to A 89 as ALA

Builds a new residue onto the end of a chain, attached to the named terminal residue and fitted against the refinement map. The type defaults to ‘auto’ (guessed from any sequence); add ‘as ALA’ to force one. With no residue named, acts on the active residue; with no model number, the active model.

autofit A/72

Auto-fit the best rotamer for a residue.

Examples:

  • autofit A/72
  • auto-fit rotamer A 72
  • autofit

Auto-fits the best rotamer for the residue against the refinement map (open a map first). With no residue named, acts on the active residue (the one at the centre of the screen).

backrub rotamer A/89

Apply a backrub rotamer fit to a residue.

Examples:

  • backrub rotamer A/89
  • backrub A 89
  • backrub rotamer

Applies a backrub rotamer fit to the named residue. With no residue named, acts on the active residue (the one at the centre of the screen).

delete residue A/72

Delete a single residue.

Examples:

  • delete residue A/72
  • delete residue A 72
  • delete residue

Deletes the named residue. With no residue named, acts on the active residue (the one at the centre of the screen).

pepflip A/89

Flip the peptide following a residue.

Examples:

  • pepflip A/89
  • pep flip A 89
  • pepflip

Flips the peptide bond following the named residue by 180. With no residue named, acts on the active residue (the one at the centre of the screen).

replace residue A/72 with ALA

Mutate a residue to another type.

Examples:

  • replace residue A/72 with ALA
  • mutate residue A 72 to GLY
  • mutate residue to ALA

Mutates the residue to the given (1- or 3-letter) type. With no residue named, acts on the active residue (the one at the centre of the screen).

Models

merge model 1 and model 2

Merge one model into another.

Merges the second model into the first, so the combined model keeps the first model’s number.

superpose model 0 onto model 1

Superpose one model onto another (SSM).

Examples:

  • superpose model 0 onto model 1
  • superpose model 0 onto model 1 in place

Superposes the source model onto the target (reference) model by secondary-structure matching (SSM). By default a superposed copy is made, leaving the source model untouched; add ‘in place’ to move the source model itself instead.

centre at 12.0 4.5 -3.2

Centre the view on an x, y, z position.

Centres the view on the given orthogonal coordinates.

go to A 45

Centre the view on a chain/residue.

Examples:

  • go to A 45
  • centre on A/45
  • go to model 0 B 12

Centres on the given chain/residue, picking a sensible atom (CA for protein, P/C1’ for nucleotides, and so on) so it works for waters, ligands and nucleic acids too. With no model number, acts on the active model. Chain and residue may be separated by a space or a slash.

next residue

Centre on the next residue.

Examples:

  • next residue
  • next
  • forward residue

Centres on the next residue after the active one (like the space bar). The active residue is the one at the centre of the screen.

previous residue

Centre on the previous residue.

Examples:

  • previous residue
  • prev
  • back residue

Centres on the residue before the active one (like shift-space). The active residue is the one at the centre of the screen.

Refinement

refine

Real-space refine the active residue.

Examples:

  • refine
  • refine active residue
  • refine here

Real-space refines the active residue (the one at the centre of the screen) against the refinement map.

refine b factors

Refine the atomic B-factors (ADPs) of a model.

Examples:

  • refine b factors
  • refine b-factors of model 0
  • refine adps

Refines the atomic B-factors (ADPs) of the whole model using the shiftfield method, against the reflection data. Needs a map with reflection data set as the refinement map (unlike real-space refinement, this is a whole-molecule reciprocal-space step). With no model number, acts on the active model.

refine chain A

Real-space refine an entire chain.

Examples:

  • refine chain A
  • refine chain B

Real-space refines a whole chain (its full residue range) against the refinement map. With no model number, acts on the active model.

refine A 45 to 50

Real-space refine a range of residues.

Examples:

  • refine A 45 to 50
  • refine A/45-50
  • real space refine A 100 to 105

Real-space refines the given residue range against the refinement map. With no model number, acts on the active model.

refine A 45

Real-space refine a single residue.

Examples:

  • refine A 45
  • refine A/45
  • refine residue B 12

Real-space refines a single residue against the refinement map. With no model number, acts on the active model.

refine sphere A/89

Real-space refine the sphere around a residue.

Examples:

  • refine sphere A/89
  • refine sphere A 89
  • refine sphere

Real-space refines the sphere of atoms around the named residue against the refinement map. With no residue named, acts on the active residue (the one at the centre of the screen).

Representation

colour carbons coloured

Use element-coloured carbons for a model.

Examples:

  • colour carbons coloured
  • coloured carbons
  • coloured carbons for model 0

Uses per-element carbon colouring. With no model number, acts on the active model.

colour carbons grey

Use grey carbon colours for a model.

Examples:

  • colour carbons grey
  • grey carbons
  • grey carbons for model 0

Uses grey for carbon atoms. With no model number, acts on the active model.

hide ribbons

Hide the ribbon representation of a model.

Examples:

  • hide ribbons
  • hide ribbons for model 0

Removes the ribbon representation added by ‘show ribbons’. With no model number, acts on the active model.

hide surface

Hide the molecular surface of a model.

Examples:

  • hide surface
  • hide surface for model 0

Removes the molecular surface added by ‘show surface’. With no model number, acts on the active model.

hide symmetry

Hide symmetry-related molecules.

show ribbons

Show a ribbon representation of a model.

Examples:

  • show ribbons
  • show ribbons for model 0

Draws a ribbon (cartoon) representation of the whole model, coloured by chain. With no model number, acts on the active model.

show surface

Show a molecular surface of a model.

Examples:

  • show surface
  • show surface for model 0

Draws a molecular surface for the whole model, coloured by chain. With no model number, acts on the active model.

show symmetry

Show symmetry-related molecules.

Session

close sequence

Close the sequence view for a model.

Examples:

  • close sequence
  • close sequence of model 0

Closes the sequence view opened by ‘open sequence’. With no model number, acts on the active model.

list maps

List the loaded maps.

Lists the loaded maps with their molecule number and name, marking which are difference maps.

list models

List the loaded models.

Examples:

  • list models
  • list molecules

Lists the loaded models with their molecule number and name.

load tutorial

Load the tutorial model and data.

Examples:

  • load tutorial
  • load tutorial model and data

Loads the bundled tutorial model and its data (map coefficients), the same as File > Open Tutorial.

open sequence

Open the sequence view for a model.

Examples:

  • open sequence
  • open sequence of model 0

Opens the sequence view for the model. Close it again with ‘close sequence’. With no model number, acts on the active model.

Settings

get bond thickness

Report the current default bond thickness.

Examples:

  • get bond thickness
  • what is the bond thickness

get contour level

Report the current contour level of a map.

Examples:

  • get contour level
  • what is the contour level of map 1

With no map number, acts on the active map.

get contour step

Report the contour-level scroll step for normal maps.

Examples:

  • get contour step
  • what is the contour step

get difference map contour step

Report the contour-level scroll step for difference maps.

Examples:

  • get difference map contour step
  • what is the difference map contour step

get font size

Report the current on-screen label font size.

Examples:

  • get font size
  • what is the font size

get map radius

Report the current map display radius.

Examples:

  • get map radius
  • what is the map radius

get map sampling rate

Report the current map sampling rate.

Examples:

  • get map sampling rate
  • what is the map sampling rate

set bond thickness to 4

Set the default bond (stick) thickness.

Examples:

  • set bond thickness to 4
  • set bond thickness 3

Line/stick thickness for model bonds, in pixels. A whole number; the default is 5.

set contour level to 1.5 sigma

Set the contour level of a map (absolute, or in sigma).

Examples:

  • set contour level to 1.5 sigma
  • set contour level of map 1 to 0.3
  • set contour level of map 1 to 2 sigma

Sets the contour level of a map, in absolute units by default or in sigma when the value ends with ‘sigma’. With no map number, acts on the active map.

set contour step to 0.1

Set the contour-level scroll step for normal maps.

Examples:

  • set contour step to 0.1
  • set contour step 0.05

How much a scroll changes the contour level of a normal (non-difference) map. See ‘set difference map contour step’ for difference maps.

set difference map contour step to 0.1

Set the contour-level scroll step for difference maps.

Examples:

  • set difference map contour step to 0.1
  • set diff map contour step 0.05

How much a scroll changes the contour level of a difference map.

set font size to 2

Set the on-screen label font size.

Examples:

  • set font size to 2
  • set font size 3

Size of on-screen labels: 1 (small), 2 (medium) or 3 (large).

set map radius to 20

Set the map display radius (Angstroms).

Examples:

  • set map radius to 20
  • set map radius 15

Radius, in Angstroms, of the sphere of density drawn around the screen centre. Larger radii are slower to contour.

set map sampling rate to 1.8

Set the map sampling rate for maps read from now on.

Examples:

  • set map sampling rate to 1.8
  • set map sampling 2

Finer sampling (higher rate) makes smoother maps at the cost of memory. Applies to maps read after it is set; typical values are 1.5-2.5.

set updating maps on

Turn Coot’s auto-updating (sfcalc) maps on or off.

Examples:

  • set updating maps on
  • set updating maps off

Turns Coot’s auto-updating maps on or off. Coot’s auto-updating maps recompute the 2Fo-Fc and difference maps from the reflection data as you edit the model, so density follows the atoms. Needs the refinement map (a map with reflection data attached) and a difference map to be loaded - ‘load tutorial’ or opening an MTZ provides both. Only one updating-maps session can run at a time.

stop updating maps

Stop Coot’s auto-updating (sfcalc) maps.

Turns off auto-updating maps (same as ‘set updating maps off’). Coot’s auto-updating maps recompute the 2Fo-Fc and difference maps from the reflection data as you edit the model, so density follows the atoms. Needs the refinement map (a map with reflection data attached) and a difference map to be loaded - ‘load tutorial’ or opening an MTZ provides both. Only one updating-maps session can run at a time.

State

undo

Undo the last action.

Undoes the last modification.

Validation

check cis peptides

Count cis peptide bonds in a model.

Examples:

  • check cis peptides
  • cis peptides

Counts cis peptide bonds. Cis peptides before proline are common and usually fine; other cis peptides are worth checking. With no model number, acts on the active model.

check clashes

List steric clashes (atom overlaps) for a model.

Examples:

  • check clashes
  • atom overlaps

Lists atom overlaps (steric clashes) with a clash volume above 2 A^3. With no model number, acts on the active model.

check gln and asn

Open the Gln/Asn side-chain flip (B-factor outlier) analysis.

Examples:

  • check gln and asn
  • gln asn outliers

Opens the Gln/Asn B-factor outlier analysis, flagging glutamine and asparagine side chains that may need a 180 degree flip. With no model number, acts on the active model.

check missing atoms

List residues with missing atoms in a model.

Examples:

  • check missing atoms
  • missing atoms

Lists residues that are missing modelled atoms. With no model number, acts on the active model.

check non-standard residues

List non-standard residue types in a model.

Examples:

  • check non-standard residues
  • non-standard residues

Lists residue types that are not standard amino acids or water - ligands, modified residues and the like. With no model number, acts on the active model.

check ramachandran

List Ramachandran outliers for a model.

Examples:

  • check ramachandran
  • ramachandran outliers

Lists residues in improbable regions of the Ramachandran plot (probability below 0.02). With no model number, acts on the active model.

check rotamers

List the least probable rotamers for a model.

Examples:

  • check rotamers
  • rotamer outliers

Reports the least probable side-chain rotamers (low probability = unusual). With no model number, acts on the active model.

check waters

List highly-coordinated waters (possible ions) in a model.

Examples:

  • check waters
  • highly coordinated waters

Lists waters with an unusually high number of close contacts (coordination number 5 or more within 3.2 A), which may be misassigned ions. With no model number, acts on the active model.

go to blob 1

Centre the view on a blob from the last ‘find blobs’ result.

Examples:

  • go to blob 1
  • centre on blob 2

Centres the view on one of the blobs from the most recent ‘find blobs’ command, numbered from 1 (largest first). Run ‘find blobs’ first to populate the list.

open validation

Open the interactive validation overlay for a model.

Examples:

  • open validation
  • validation overlay

Opens Coot’s interactive validation overlay (Ramachandran, rotamers, density fit and more) for a model against the active map. With no model number, acts on the active model. With no map number, acts on the active map.

difference map peaks

Mark peaks in the difference map (missing/wrong density).

Examples:

  • difference map peaks
  • difference map peaks above 4 sigma

Marks peaks in the Fo-Fc difference map - candidate sites for missing atoms, waters or ligands, and for parts of the model in wrong density. Uses a 4 sigma cut-off by default. Needs a difference map to be loaded. With no model number, acts on the active model.

validate anomalies

Summarise model outliers (Ramachandran, clashes, C-beta, chirals).

Examples:

  • validate anomalies
  • find outliers

Summarises geometry outliers - Ramachandran improbables, atom overlaps (clashes), C-beta deviations and chiral volume errors - as text. With no model number, acts on the active model.

find blobs

Summarise unmodelled density blobs (candidate build sites).

Examples:

  • find blobs
  • check unmodelled blobs
  • find blobs above 2 sigma

Lists peaks of density not accounted for by the model - candidate sites for waters, ligands or unbuilt residues. The search masks out density within 1.9 A of the model and finds the peaks left over, so it belongs on a difference (mFo-DFc) map: by default it uses the loaded difference map at a 3.0 sigma cut-off. On a 2mFo-DFc map almost everything is above a low cut-off, so blobs would appear all over - name a map with ‘using map N’ only if you mean to. Add e.g. ‘above 2 sigma’ to change the threshold.

View

rock

Toggle rocking the view.

Toggles idle rocking; issue again to stop.

background black

Set the background colour.

Examples:

  • background black
  • set background colour to white

Colour names: black, white, grey, and the other named colours accepted by colour commands.

orthographic

Switch between orthographic and perspective projection.

Examples:

  • orthographic
  • perspective view

zoom to 30

Set the view zoom factor.

Examples:

  • zoom to 30
  • set zoom 50

Larger numbers zoom out. Typical range ~10-100.

spin

Toggle spinning the view.

Toggles idle spinning; issue again to stop.

fullscreen

Toggle fullscreen mode.

Toggles fullscreen; issue again to leave fullscreen.