molviewer

(To be removed) Display and manipulate 3-D molecule structure

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molviewer will be removed in a future release.

Syntax

molviewer(File)

molviewer(pdbID)

molviewer(pdbStruct)

figureHandle = molviewer(___)

Description

molviewer(File) reads the data in a molecule model file, File, and opens Molecule Viewer displaying the 3-D molecular structure for viewing and manipulation.

example

molviewer(pdbID) retrieves the structural data of a protein, pdbID, from the PDB database and opens Molecule Viewer displaying the 3-D molecular structure for viewing and manipulation.

example

molviewer(pdbStruct) reads the data from pdbStruct, a structure containing a field for each PDB record, and opens Molecule Viewer displaying a 3-D molecular structure for viewing and manipulation.

example

figureHandle = molviewer(___) returns the figure handle of Molecule Viewer.

example

Examples

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View H5N1 Virus Hemagglutinin Molecule with Molecule Viewer

View the H5N1 influenza virus hemagglutinin molecule, whose structural information is located at www.rcsb.org/pdb/files/2FK0.pdb.gz.

Open the H5N1 influenza virus hemagglutinin molecule in Molecule Viewer.

molviewer('https://www.rcsb.org/pdb/files/2FK0.pdb.gz');

View the molecule with a PDB identifier of 2DHB.

molviewer('2DHB');

View the molecule with a PDB identifier of 4hhb, and create a figure handle for Molecule Viewer.

FH = molviewer('4hhb')

FH = 

  Figure (BioinfoMolviewer) with properties:

      Number: 5
        Name: 'Molecule Viewer: Blank'
       Color: [0.9400 0.9400 0.9400]
    Position: [1000 818 560 420]
       Units: 'pixels'

  Show all properties

Use the getpdb function to retrieve protein structure data from the PDB database and create a MATLAB^® structure. Then view the protein molecule.

pdbstruct = getpdb('1vqx')
molviewer(pdbstruct)

pdbstruct = 

  struct with fields:

               Header: [1×1 struct]
                Title: [2×60 char]
             Compound: [5×28 char]
               Source: [4×58 char]
             Keywords: 'HELIX-LOOP, SIGNALING PROTEIN'
       ExperimentData: 'SOLUTION NMR'
              Authors: 'O.G.KISSELEV,M.A.DOWNS,J.H.MCDOWELL,P.A.HARGRAVE'
         RevisionDate: [1×4 struct]
           Superseded: [1×1 struct]
              Journal: [1×1 struct]
              Remark2: [1×1 struct]
              Remark3: [1×1 struct]
              Remark4: [2×59 char]
            Remark100: [3×59 char]
            Remark210: [30×59 char]
            Remark215: [6×59 char]
            Remark300: [6×59 char]
            Remark350: [13×59 char]
            Remark470: [13×59 char]
            Remark500: [33×59 char]
            Remark900: [5×59 char]
         DBReferences: [1×1 struct]
    SequenceConflicts: [1×7 struct]
             Sequence: [1×1 struct]
     ModifiedResidues: [1×7 struct]
            Heterogen: [1×7 struct]
        HeterogenName: [1×2 struct]
     HeterogenSynonym: [1×2 struct]
              Formula: [1×2 struct]
                Helix: [1×1 struct]
                 Link: [1×11 struct]
               Cryst1: [1×1 struct]
              OriginX: [1×3 struct]
                Scale: [1×3 struct]
                Model: [1×15 struct]
         Connectivity: [1×58 struct]
               Master: [1×1 struct]
            SearchURL: 'https://files.rcsb.org/download/1vqx.pdb'

Input Arguments

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`File` — Molecule model file name
character vector | string

Character vector or string specifying one of the following:

File name of a file on the MATLAB search path or in the MATLAB Current Folder
Path and file name
URL pointing to a file (URL must begin with a protocol such as http://, ftp://, or file://)

The referenced file is a molecule model file, such as a Protein Data Bank (PDB)-formatted file (ASCII text file). Valid file types include:

PDB
MOL (MDL)
SDF
XYZ
SMOL
JVXL
CIF/mmCIF

Example: 'https://www.rcsb.org/pdb/files/2FK0.pdb.gz'

`pdbID` — Unique identifier for protein structure record
character vector | string

Unique identifier for a protein structure record in the PDB database specified as a character vector or string.

Note

Each structure in the PDB database is represented by a four-character alphanumeric identifier. For example, 4hhb is the identifier for hemoglobin.

Example: '2DHB'

`pdbStruct` — PDB record structure
structure

A structure containing a field for each PDB record, such as returned by the getpdb or pdbread function.

Output Arguments

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`figureHandle` — Molecule Viewer figure handle
figure handle

Figure handle of Molecule Viewer.

Tips

You can pass the figureHandle to the evalrasmolscript function, which sends RasMol script commands to Molecule Viewer.
If you receive any errors related to memory or Java^® heap space, try increasing your Java heap space as described at https://www.mathworks.com/matlabcentral/answers/92813-how-do-i-increase-the-heap-space-for-the-java-vm-in-matlab.
After displaying the 3-D molecule structure, you can:
- Hover the mouse over a subcomponent of the molecule to display an identification label for it.
- Spin and rotate the molecule at different angles by click-dragging it.
- Spin the molecule in the x-z plane by clicking .
- Spin the molecule in the x-y plane by pressing and holding the Shift key, then click-dragging left and right.
- Zoom in by pressing and holding the Shift key, then click-dragging up and down.
- You can also zoom in by clicking the figure, then turning the mouse scroll wheel, or by clicking the following buttons:
  or
- Move the molecule by pressing and holding Ctrl + Alt, then click-dragging.
- Change the background color between black and white by clicking .
- Reset the molecule position by clicking .
- Show or hide the Control Panel by clicking .
- Manipulate and annotate the 3-D structure by selecting options in the Control Panel or, for a complete list of options, by right-clicking the Molecule Viewer window to select commands:
- Display the Jmol Script Console by clicking .
  
  Note
  There is a known bug with the Open button of the script editor that prevents loading a Rasmol script interactively. Instead use the evalrasmolscript function which sends RasMol script commands to Molecule Viewer. Also, you can copy and paste the script commands into the script console.