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Molmil manual

Cite molmil

If you use Molmil, please cite our Molmil paper.

UI

3D operations

  • Rotate: hold left mouse button and drag
  • Translate (x/y): (hold left+right mouse button, or hold scroll button, or hold left mouse button + shift key) and drag
  • Zoom (z): hold right mouse button and drag
  • Rotate around atom: left-click atom, then hold Ctrl while holding left mouse button and dragging to rotate

Atom/bond information

  • Left-click on an atom to select, right-click to show a context menu
  • Calculate distance between two atoms: Left click on first atom, Ctrl+left click on second atom
  • Calculate angle between three atoms: Left click on first atom, Ctrl+left click on second atom, Ctrl+left click on third atom
  • Calculate dihedral between four atoms: Left click on first atom, Ctrl+left click on second atom, Ctrl+left click on third atom, Ctrl+left click on fourth atom

Menu operations

  • Show list of files/chains/residues (Structures menu):
    Left mouse click on the right-side menu (>>>), click on the files/chains to see the underlying chains/residues.
    Right click on the files/chains/residues to modify the styling

  • Toggle structures/chains:
    Ctrl + left-click on a structure/chain in the Structures menu

  • Show information about atom and show the styling menu (can be used to style corresponding residue/chain and display nearby residues): right click on any atom in the canvas

  • Open a file from the local drive:
    Drag-and-drop files from the local drive into the Molmil window

  • Save PNG:
    Molmil menu -> Save -> PNG image

  • Settings:
    Molmil menu -> Settings (quality, loop/sheet smoothing, fog, projection mode, color scheme, background color)

  • Slab:
    Molmil menu -> Settings -> Slab

  • Show Biological Unit:
    Molmil menu -> View -> Configure BU (for structures that contain BU metadata)

  • Animation (PDB model or MD trajectory):
    Molmil menu -> Animation

  • Full screen:
    Molmil menu -> Enable full-screen

  • WebVR:
    Molmil menu -> Enable WebVR (on compatible platforms only)

  • Show Command line interface:

    1. Molmil menu -> Toggle CLI
    2. "<" button in the bottom left corner
    3. Press ESC button twice in quick succession to toggle the CLI and move the cursor there (when showing the CLI)

  • Clear all loaded files:
    Molmil menu -> Clear
    (Refreshing the page also works)

  • Toggle waters:
    Open the Structures menu (top right >>>) -> click the 3 dots -> Show/Hide waters

  • Toggle hydrogens:
    Open the Structures menu (top right >>>) -> click the 3 dots -> Show/Hide hydrogens

Style interface

  • Enable interface: Molmil menu -> Style IF

  • Change tabs In the Style IF panel, click [Style menu], and then choose one of the available options

  • Hide panel In the Style IF panel, click [Style menu], and then choose "Hide"

  • Resize panel In the Style IF panel in the bottom right corner, left-click and drag on the resize icon (diagonal line) and drag upwards to make the panel smaller and downwards to make it larger

Add a label to a file/chain/residue/atom:

  1. Right click on a file/chain/residue -> Label
  2. Any atom in the canvas -> Label -> Atom/Residue/Chain

Pymol commands

select

Select atoms by using an expression: select _name_, expression

expression

  • name: select by atom name
  • symbol: select by element name
  • resn: select by residue name
  • resi: select by residue id
  • ss: select by secondary structure (h: helix, s: sheet, l: loop)
  • chain: select by chain name
  • hydro: select waters
  • hetatm: select ligands
  • backbone: select protein backbone atoms
  • sidechain: select protein sidechain atoms
  • model: select by filename/fileid
  • and/or: combine multiple selections

examples:

  1. select carbon atoms:
    select carbons, symbol C
  2. select the backbone heavy atoms:
    select sidechain_12, resi 12 and sidechain

color

Color a group of atoms: color clr, atom-list/expression

clr can be either a colorname, a hex value (starting with #) or an rgb(a) value in the shape of [r, g, b, a], where r,g,b,a is an integer between 0-255

atom-list is either a _name_ object (defined by a select command) or an expression as used by a select command

Examples:

  • color red, sidechain_12
  • color red, resi 12 and sidechain
  • color [255, 255, 255], resi 12 and sidechain

cartoon_color

Color the cartoon representation of a group of atoms: cartoon_color, atom-list/expression

set_color

Define a new named color: set_color _color_name_, [r, g, b, a]

show

Show atoms: show _repr_, atom-list/expression
_repr_: spheres, ball_stick, sticks, lines, cartoon, ca-trace, label

hide

Hide atoms: hide _repr_, atom-list/expression
_repr_: hydro, all, cartoon, snfg-icon, solvent, coarse-surface, spheres, ball_stick, sticks, lines, cell, label

enable

Show file/model enable model #1 enable file.pdb

disable

Hide file/model disable model #1 disable file.pdb

turn

Rotate the camera/system: turn axis, degrees
axis: x, y, z

move

Translate the camera/system: move axis, Angstrom
axis: x, y, z

translate

Translate a selection of atoms along an axis: translate [x,y,z], atom-list/expression

fetch

Fetch a PDB entry from PDBj: fetch pdbid

fetch-cc

Fetch a chem_comp entry from PDBj: fetch comp_id

fetch-chain

Fetch a specific chain from a PDB entry from PDBj: fetch entryId

efsite

Fetch an efsite entry from PDBj: efsite entryId

load

Load a file: load location, _options_
location can be either a file path on the local hdd (requires the local version of Molmil, cannot run via the web version), or a URL
_options_ is a comma-separated list of options, e.g. format=pdb,gzipped=1, indicates that the file format is a gzipped pdb flat-file (molmil normally determines this from the file extension, but when loading a file that misses a file extension, e.g. when loading the output from a REST API, this information needs to be supplied)

mplay

Plays a trajectory: mplay

mstop

Stops playing a trajectory: mstop

origin

Set the origin to a specific set of atoms: origin selection

set

Set various settings

Set the radius of the sticks for a group of atoms: set stick_radius, value, atom-list/expression

Enable fog: set depth_cue, 1
Disable fog: set depth_cue, 0

Settings:

  • stick_radius float
  • depth_cue 1/0
  • cartoon_highlight_color 1/color
  • field_of_view float
  • orthoscopic on/off
  • label_bg_color color
  • label_outline_color color
  • label_color color
  • label_border on/off
  • label_position (dx,dy,dz)
  • label_atom_center all OR atom name
  • label_size float
  • label_front 1/0
  • cartoon_smooth_loops int
  • all_states on/off
  • movie_mode forward/backward/swing/swing-once
  • edmap_sigma float
  • mesh_color color
  • surface_color color
  • cif_use_auth on/off
  • stereo_mode 10(anaglyph)/5(side-by-side)/2(cross-eyed)
  • connect_cutoff float
  • backface_cull 1/0

Here, color is either a pre-configured color name, or an rgba array: [r,g,b,a], e.g. [255, 0, 0, 255] for red

bg_color

Set the background color: bg_color color

label

Set a label to a set of atoms: label selection, label-name

save

Save the loaded structure: save file.pdb, selection, snapshot, format

viewport

Resize the viewport (screen size): viewport width, height

view

Recall or store a specific view: view key, action action: recall, store

Save the current view as "test": view test, store
Recall (restore) the view "test": view test

reset

Resets the camera the default position and orientation (identity matrix, but zoomed out to show the molecules)

findseq

Finds a specific sequence: findseq sequence, selection, name

delete

Delete a set of atoms: delete selection
Delete chain A: delete chain A

edmap

Fetch the electron density map of the loaded entry for a specific region: edmap selection, border
Show the electron density for all ligands and nearby region (5 A): edmap hetatm, 5

frame

Select a specific frame (NMR-model / MD trajectory), starting from 1: frame modelId
Select 10th frame: frame 10

bond

Create a bond between two atoms: bond selection1, selection2, bondOrder
Create a peptide bond between residue 32 and residue 1: bond resi 32 and name C and resi 1 and name N, 1

stereo

Set a stereo mode: stereo mode
Where mode is any of; off, crosseye, sidebyside, anaglyph
Enable sidebyside mode: stereo sidebyside

orient

Focus the camera on a specific selection with optimized orientation: orient selection
Orient on chain A: orient chain A
Orient on whole system: orient

alter

Alter properties of atoms: alter selection, setting=value
Set B-factor of residue: alter resi 32, b=0.5

indicate

Indicate the selection on the screen: indicate selection
Indicate chain A: indicate chain A

png

Output a PNG image to a file: png filename
Copy a PNG image onto the clipboard: png

repr

Quick select representation Examples:

  • repr au
  • repr bu

style-if

Show style interface
Examples:

  • style-if structure
  • style-if bu
  • style-if edmap
  • style-if sites
  • style-if align
  • style-if settings
  • style-if hide

align

Superposes two chains
align struc1:chain1, struc2:chain2
align file1.pdb:A, file2.pdb:B

quit

Exit molmil-app.