• Jmol Commands
• Jmolly
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I. Creating Surfaces

Molecular surfaces can be calculated by Jmol, but for large molecules this can be quite CPU intensive and time consuming to do on the fly. It is therefore not prudent to do this in web pages devoted to macromolecules, unless one is interested in displaying the surface of only a small subset of residues or atoms.

One can, however, use the Jmol applet to calculate a surface for a large molecule, save the isosurface calulations in a *.jvxl file (JVoxel format), and quickly load the pre-calculated surface view (*.jvxl) using Jmol commands in a web page. One approach for doing this is outlined below, followed by a table with sample Jmol buttons and commands used to manipulate surface views.

• Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only Web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar.
• The Jmol application/applet is open-source software (i.e., the software and source are freely available for use and for developement) that is designed to display chemical molecules. It is similar in appearance and operation to RasMol. See below for a list of examples of Jmol use in the Penn X-ray Facility.

• To begin, open your Jmol Applet (Jmol.jar). Versions 11.2 and up are recommended for full implementation of features below. Load a molecule of choice. Open the scripting window of the applet for command entry.
• Select the portion of your molecule you wish to display the surface of (e.g., 'select nucleic' or 'select ligand').
• Use one of the 'isosurface' commands (see below) to calculate the molecular surface of the selected molecule/s.
• Use the 'write isosurface filename.jvxl' command to save the surface in a Jvxl file (this will save into the directory of your Jmol applet).
• Copy the Jvxl file into the directory of the web page you are building so that the path to the Jvxl file can be easily linked. An example jvxl file can be seen here.
• Use 'isosurface 'filename.jvxl' ' to load the surface.

(a) Judgment as a Matter of Law. If a party has been fully heard on an issue during a jury trial and the court finds that a reasonable jury would not have a legally sufficient evidentiary basis to find for the party on that issue, the court may. One can, however, use the Jmol applet to calculate a surface for a large molecule, save the isosurface calulations in a.jvxl file (JVoxel format), and quickly load the pre-calculated surface view (.jvxl) using Jmol commands in a web page. One approach for doing this is outlined below, followed by a table with sample Jmol buttons and commands. Jmol is an open-source Java viewer for three-dimensional chemiscal structures, with features for chemicals, materials and biomolecules. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs 1.

Different types of surfaces may be specified (for more detail, see the Jmol Interactive Scripting Docs):

• The solvent excluded surface ('isosurface solvent') is determined by rolling a probe solvent atom on the molecule at the distance of the van der Waals radii of the atoms. Radius of the spherical probe (in Angstroms) may be specified (default is 1.2). 'isosurface molecular' sets a probe radius of 1.4.
• The solvent accessible surface ('isosurface sasurface') is a contour of the center of the probe as it is rolled on the molecule of interest. The probe radius may be specified.
• Cavities may be depicted ('isosurface cavity').
• Molecular Electrostatic Potential surfaces are described below.

II. Mapping Properties on Surfaces

A. Common Properties

Jmol makes it possible to map onto a surface any property for which data are available in a file being viewed. Data on the following properties is comonly found in PDB files: temperature, surfacedistance, atomno, elemno, charge.

So, for example, temperature (~mobility), stored in the B-factor column of a PDB file, can be mapped according to a graded color scheme of choice. Graded color schemes in Jmol can be found here. The most commonly used are: roygb(red -> orange -> yellow -> green -> blue); bgyor (blue -> green -> yellow -> orange -> red); rwb (red -> tints of red-pink -> white -> tints of blue -> blue); bwr (blue -> tints of blue -> white -> tints of pink-red -> red).

B. Molecular Electrostatic Potential

Unfortunately, PDB files do not contain the partial charge data that would allow for the calculation of Molecular Electrostatic Potential (MEP) surfaces. Fortunately, there are ways to generate these surfaces. Here, we describe one such method.

1. Generate a 'PQR' file from a PDB file.

A PQR file is like a PDB except that it contains partial charge data in what was the B-factor column and contains atomic radii data. We first recommend removing waters from your PDB, either by editing the PDB file directly in a word processor (easiest! - just remember to save your edited file as text with a pdb extension and be sure to add a REMARK line saying you removed the waters), or by using any number of molecular visualization programs (e.g. Jmol, DS Visualizer {Accelerys}, PyMol, HyperChem, etc.).

To generate a PQR, you can use the PDB2PQR server, or get the GEMSTONE application and use PDB2PQR through GEMSTONE. A GEMSTONE tutorial is available. The PDB2PQR program runs a molecular dynamics (MD) simulation. Several MD force fields are available. We normally use PARSE. If you are interested, here is a tutorial on MD.

Here is a comparison of a residue in a PDB file and the corresponding residue in a generated PQR file. Note that the last two columns are now partial charge and radius data. Note also that hydrogens have been generated.

2. Render a MEP surface in Jmol and use this surface with a PDB in your web page.

• Open your Jmol Applet (Jmol.jar). Open the scripting window of the applet for command entry. Load your generated PQR of step 1.
• Create a MEP surface, color coded. This can use various combinations of commands (you may want to consult the Jmol Interactive Scripting Docs). An example would be 'isosurface name molecular color absolute -.5 .5 colorscheme rwb MAP mep'. You will get a message giving the data range. For example, 'isosurface full data range -0.006000088 to 2.358699.' In this case you would change your data range to, for example: 'isosurface name molecular color absolute -.006 2.4 colorscheme rwb MAP mep'. The calculation takes some time for large molecules. Note: MEPs are commonly displayed with a rwb color scheme gradient (red=negative, white=neutral, blue=positive).
• Use the 'write isosurface filename' command to save the surface in a Jvxl file (this will save into the directory of your Jmol applet).
• Copy the Jvxl file so generated into the directory of the web page you are building so that the path to the Jvxl file can be easily linked.
• You can now load your PDB in your web page as you normally would. Use 'isosurface 'filename' ' to load the MEP surface.

Jmol Commands

Here is an example. Note how the RNA (with a negatively charged oxygens in its sugar-phosphate backbone) is wrapped around the positively charged portion of the surface of this protein.

Note: if this tutorial is helpful in the creation of your own webpages, please explicitly acknowledge your use of this page (URL, Author, date accessed, and a link to this page) in your webpage/s. And please drop an email to marcey@callutheran.edu with a link to your page/s. This helps with funding opportunities for the OMM and helps ensure continued development of this resource. Thanks!

Jmol is computer software for molecular modellingchemical structures in 3-dimensions.^[2] Jmol returns a 3D representation of a molecule that may be used as a teaching tool,^[3] or for research e.g., in chemistry and biochemistry.It is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License (LGPL) version 2.0. A standalone application and a software development kit (SDK) exist that can be integrated into other Java applications, such as Bioclipse and Taverna.

A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways.For example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc.^[4]Jmol supports a wide range of chemical file formats, including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile (mol), and Chemical Markup Language (CML). There is also a JavaScript-only (HTML5) version, JSmol, that can be used on computers with no Java.^[5]

The Jmol applet, among other abilities, offers an alternative to the Chime plug-in,^[3] which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, the Sculpt mode. Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS 9. Jmol requires Java installation and operates on a wide variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, and Safari.

Screenshots[edit]

• Crystal structure of an H/ACA box RNP from Pyrococcus furiosus.

• Highlighting two salt bridges in hemoglobin tetramer (hemo group as sticks at bottom-right).

• A fragment of transcription factor TFIIIA forming three consecutive zinc finger motifs, bound to a stretch of DNA.

• Eubacterial 70S Ribosome from Thermus thermophilus.

Jmolly

See also[edit]

• Chemistry Development Kit (CDK)

References[edit]

1. ^Jmol translations
2. ^Chen, Jim X. (2008), Springer (ed.), Guide to Graphics Software Tools, p. 471, ISBN978-1-84800-900-4
3. ^ ^abHerráez, A (2006), 'Biomolecules in the Computer: Jmol to the Rescue', Biochemistry and Molecular Biology Education, 34 (4): 255–61, doi:10.1002/bmb.2006.494034042644, PMID21638687, S2CID36319720
4. ^Herráez, A (2007), Lulu (ed.), How to Use Jmol to Study and Present Molecular Structures, Volume 1, p. 21, ISBN978-1-84799-259-8
5. ^'JSmol'. Archived from the original on 2018-01-01. Retrieved 2015-11-02.

Jmol Law

External links[edit]

• Official website
  • Wiki with listings of websites, wikis, and moodles
• Willighagen, Egon; Howard, Miguel (June 2007). 'Fast and Scriptable Molecular Graphics in Web Browsers without Java3D'. Nature Precedings. doi:10.1038/npre.2007.50.1.

Jmol 3d