Visualize

This module translates visualization scripts to the script language of MMM and can directly execute them in MMM. For direct execution, MMM must be open in the same Matlab instance. This is intended for convenient and consistent visualization of ensembles generated by MMMx. Population of conformers is encoded by transparency or coil radius.

getens

Input of an ensemble in MMMx ensemble list format.

getens file
Arguments
  • file - file name, extension .ens is appended if there is none

Remarks
  • there should be only one getens line, or, alternatively, an addpdb line, or an import line

addpdb

Input of an ensemble via PDB files matching a pattern. This can also be used for visualizing a single conformer

addpdb files
Arguments
  • files - file name that can include wildcards, e.g. hnRNPA1_sorted_m*.pdb

Remarks
  • all populations are equal

  • each PDB file should hold only a single conformer or, alternatively, there should be only one PDB file with all conformers

  • there should be only one addpdb line, or, alternatively, a getens line or an import line

import

Inmport an ensemble from PDB via its PDB identifier. This can also be used for loading a single PDB file.

import pdbid
Arguments
  • pdbid - PDB identifier, e.g. 2LZM, can also be a PDB file name, but then must have extension .pdb

Remarks
  • if the PDB file has several conformers, all populations are set equal

  • there should be only one import line, or, alternatively, a getens line or a addpdb line

figures

Sets a general output format for saving graphics.

figures format
Arguments
  • format - figure output format, such as png, pdf, bmp, jpeg, tiff

Remarks
  • default is png

  • figure format can also be specified in individual graphics commands

normalize

Normalization mode for translation of populations to transparency. If on (default), the conformer with maximum population is completely opaque and opaqueness of other conformers is proportional to the ratio of their population to the maximum population. If off, opaqueness equals population. The same normalization applies to coil radius in mode snake of keyword show.

normalize mode
Arguments
  • mode - can be on or off

script

Sets name of the MMM script file. Extension .mmm is added if there is none.

script file
Arguments
  • file - file name for the script file

Remarks
  • default is MMMx.mmm

execute

Requests direct execution of the visualization script in MMM.

execute
Remarks
  • MMM must be open in the same Matlab instance

  • MMM is reinitialized, i.e., all models and existing visualization are deleted

graphics

Request to save a graphic to a file or to copy it to the clipboard

graphics [file [mode [view]]]
Arguments
  • file - file name for the graphics file, must include extension if you need one

  • mode - graphics mode, such as png, pdf, bmp, jpeg, tiff

  • view - specification of viewing direction

Remarks
  • if there are no arguments, the current graphics is copied as a bitmap to the clipboard (Windows only)

  • if the graphics mode is missing, it is specified by the figures keyword; if this is also missing, it is png

  • view can be a Cartesian direction (x, -x, y, -y, z, -z)

  • alternatively, view can specifiy a viewing vector by three numbers, for instance 0.707 0.707 0 for halfway between x and y

  • view can also be specified by six numbers; then, the final three numbers define the camera up direction

  • use symmetry or bilayer in the prepare module for convenient coordinate transformations

  • if you have a template with your prferred viewing orientation, use superimpose in the EnsembleAnalysis module for transformation

show

Define graphics elements. All conformers in the ensemble have the same graphics elements; only transparency or width differs.

show address mode
Arguments
  • address - MMM address of chains, residues, or atoms, use (:) for all chains

  • mode - display mode, e.g., ribbon, such as graphics (:) ribbon

Remarks
  • all functionality of the show command of MMM is available

  • in general, opacity (1-transparency) is proportional to population of conformers

  • an additional mode snake displays coils with radius proportional to population

  • in snake mode, all conformers are fully opaque, transparency is not used

label

Generates and attaches spin label rotamers for later visualization.

label address type
Arguments
  • address - MMM address of a residue (labelling site), e.g. (A)131

  • type - label type, defaults to mtsl

Remarks
  • the label is only generated, not shown, use show address label for visualizing the rotamer cloud

density

Add a density surface from an MMMx density file generate by module Locate or EnsembleAnalysis.

density file [level [opacity [rgb]]]
Arguments
  • file - name of a MMMx density file, generate such files with the density keyword in EnsembleAnalysis

  • level - fraction of total density enclosed by the isosurface, defaults to 0.5

  • opacity - opacity of the isosurface, 1 is completely opaque, 0 is invisible, defaults to 0.5

  • rgb - rgb specifier, either three numbers between 0 and 1 for red, green, blue or SVG color name

Remarks
  • see SVG color table for available colors

  • rgb defaults to 0.75 0 0, which is a darkish red

color

Set color of graphics elements. All conformers in the ensemble have the same coloring; only transparency differs.

color address rgb
Arguments
  • address - address of objects of a conformer, e.g. (A)58-154 for residues 54-154 of chain A

  • rgb - rgb specifier, either three numbers between 0 and 1 for red, green, blue or SVG color name

Remarks
  • color (A)455-531 0.0 1.0 1.0 will set a cyan color (0% red, 100% green, 100% blue)

  • color (A)455-531 forestgreen will set SVG color forestgreen

  • see SVG color table for available colors

colorscheme

Set color scheme of graphics elements. All conformers in the ensemble have the same coloring; only transparency differs.

colorscheme address scheme
Arguments
  • address - address of objects of a conformer, e.g. (A)58-154 for residues 54-154 of chain A

  • scheme - one of the color schemes available in MMM, see Remarks

Remarks
  • the following remarks explain the available schemes

  • secondary - standard metal colors to secondary structure elements in ribbon plots (helices: copper, sheets: steelblue, loops: gold)

  • sequence - rainbow colors from blue to red within a chain starting from the N terminus to the C terminus

  • charge - rainbow colors from blue to red according to charge. Dark blue: +2, blue +1, grey 0, red: -1, dark red: -2

  • hydropathy - rainbow colors from blue to red according to hydropathy, with the blue end corresponding to the most hydrophilic and the red end to the most hydrophobic residues

  • helix _ propensity - rainbow colors from blue to red according to helix propensity, with the blue end corresponding to residues that tend to form and alpha helix and the red end to helix-breaking residues (Pro). Color grade is proportional to the square root of helix propensity

  • sequence can be used with two additional arguments, address of the first residue and number od residues for the color grade

  • if sequence is used with additional arguments, all residues before and after the indicated segment are colored blue and red, respectively