See examples of AniMol visualizations using different file formats and styles.

Import PDB with style

The alpha-1-antitrypsin is a protease inhibitor of the serpin family, consisting an extensive beta-sheet core flanked by several alpha-helices.
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Permanent QR code for visualization

Instructions

Importing molecules from a database is easy:

  • Go to "Create" page -> Press "Import" -> Press "PDB".
  • Enter a valid pdb code (eg 6ghj).
  • If the molecule with that code is importable, you will now see an it with the default style added.

The perspective (style) you upload your molecule is what everyone will see:

  • Change the angle by dragging.
  • Change the zoom with scroll wheel or pinch.
  • Change draw style by pressing the connected dots.
  • Change perspective by pressing the eye.
  • Remember to check "Download QR code" if you want to find your upload again!
  • Pressing "Upload" saves the molecule to the AniMol server.

You can apply a consitent style by giving AniMol a style file (advanced):

  • Hover over or interact with the molecule displayed on the window to display all the options.
  • Select the download button -> press "Download data" -> unzip file.
  • The styleN.json file describes the style, and can be provided when making future uploads to ensure they are styled consistently.

Upload movie with several .pdb

2VL0 is an integral membrane protein (a bacterial protein of 1605 residues) that operates as a pentameric ligand-gated ion channel (pLGIC); it consists of an extracellular domain of mainly beta-sheets and a membrane-embedded domain of mainly comprising alpha-helices, together forming an ion-channel. The mechanisms of ion permeation and channel gating are not yet completely understood but it is clear that a conformational change is required for function.
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Permanent QR code for visualization

Instructions

Several pdb or cif files can be uploaded simultaneously to create a 3d movie.

To specify the order of the uploaded files, a movie plan file can be used. To see an example:

  • Hover over or interact with the molecule displayed on the window to display all the options.
  • Select the download button -> press "Download data" -> unzip file.
  • You will see many x.pdb files where x is an integer, and also the movie.plan file.

The movie plan contains all the x.pdb files specifying the order. The movie.plan must contain all the x.pdb files and must only contain file names which exist. A movie.plan must also include a blank line; the file BEFORE the blank line is the 1st that will be used in the 3d movie. Note, there can only be 1 blank line, and it must not be located on the 1st line. To upload your own files with a movie plan:.

  • Go to "Create" page -> Press "Upload" -> Press "PDB".
  • Press "Load PDB files" and add all the x.pdb files.
  • Press "Load movie plan" and add the movie.plan.
  • Note that the preview you will see before uploading will not use the movie plan file. It will only be used once the upload has been completed.

Movie plan files work the same way with both pdb and cif files

Upload trajectory with .dcd and .psf

The viral spike protein of SARS-CoV-2 is of particular interest from a drug- and vaccine-development perspective due to its involvement in recognition and fusion of the virus with its host cell. It is a heavily glycosylated homotrimer, anchored in the viral membrane. It projects from the membrane giving the virus its characteristic crown-like shape. Here we see it being energetically minimized and then briefly thermalized.
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Permanent QR code for visualization

Instructions

Instead of uploading individual "frames" (multiple pdb or cif files), a dcd file with a psf file can be uploaded, which can contain a whole trajectory. For an example:

  • Hover over or interact with the molecule displayed on the window to display all the options.
  • Select the download button -> press "Download data" -> unzip file.
  • You will see the files 0.dcd and 0.psf

FAQ