3D Molecular Structure Jmol and UCSF Chimera viewers in Jalview
Channel: Jalview & Dundee Resource Online Training
Date: 2020-03-27

Jalview is a free-to-use sequence alignment and analysis visualisation software linking genomic variants in DNA, protein alignments and 3D structure (http://www.jalview.org/). In this tutorial, Jalview’s 3D molecular structure visualization capabilities are demonstrated.

There are two 3D molecular structure visualizations options, Jmol and Chimera, both seamlessly interacts with all the Jalview windows. For more information about Jmol, we recommend you visit the Jmol web site at http://www.jmol.org. Chimera, developed at the University of California, San Francisco, has to be installed separately from the UCSF website at https://www.cgl.ucsf.edu/chimera/download.html.

The Jmol structure viewer sits within the Jalview desktop and the Chimera viewer sits outside the Jalview desktop. To select either the Jmol or Chimera viewer, go to the Tools menu in the desktop window and select Preferences submenu, on the Structure tab and select the viewer you require.

Jalview can load Protein Data Bank format files directly or access them from the Protein Data Bank (http://www.rcsb.org/pdb). Note that the PDB sequence fetcher window and the Structure Chooser window provides a smart technique for selecting structures by querying the meta-data of structures.

PDB id 1A70 and 3A6S and link http://www.jalview.org/examples/exampleFile.jvp. are used in this tutorial.
 This exercise can be found in our User Manual, available to download from the Jalview website (http://www.jalview.org/about/documentation). Other Jalview training videos can be viewed in the training section of the website (http://www.jalview.org/training/Training-Videos).

Jalview can access a wide range of databases including PFAM, PDB, EMBL and UniProt. It can read a variety of file formats including FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm.
Jalview collaborates with several groups to offer a broad range of sequence analysis tools including: 
• multiple sequence alignment using Clustal Omega, Muscle, MAFFT, ProbCons, T-COFFEES, ClustalW, MSA Prob and GLProb
• tree calculations and principal component analysis (PCA)
• consensus, conservation, and functional site analysis
• secondary structure and disorder predictions
• visualisation of 3D structure.

Jalview (http://www.jalview.org/) has been developed in Geoff Barton's group (https://www.compbio.dundee.ac.uk/) in the School of Life Sciences (https://www.lifesci.dundee.ac.uk/) at the University of Dundee with the funding support of the BBSRC and the Wellcome Trust.

This video was produced by Dr Suzanne Duce, School of Life Sciences, University of Dundee.