Dear users, JMol has been tightly integrated into the protein alignment program supporting 3D-superposition and multiple 3D sequence alignments of peptide chains or even entire multiprotein complexes.
Please evaluate the system by clicking the following demo: http://www.bioinformatics.org/strap/strap.php?script=http%3A%2F%2Fwww.bioinformatics.org%2Fstrap%2FPDF%2F2003%2FPMID12595256%2F6.txt&v3d=jmol&aligner=neobio It will launch an interactive Web-start application with JMol. Running it for the first time, the view will slowly build up. The delay is because large amounts of data (4MB) are loaded from several resources. First you will see three Uniprot sequences since these small protein files are quickly downloaded from the Uniprot repository. Once the large PDB files have been downloaded, you will see three 3D-superimposed peptide chains in JMol. The 3D- and sequence alignments are based on 3D-superposition of cAlpha atoms. Strap is driven by Drag-and-drop: you can insert further 3d-models into the view by dragging protein objects or files into the Jmol view with the mouse. You can also drag sequence features into Jmol to observe the 3D-location of mutations, phosphorylation, glycosylation ... sites. These sequence features are indicated by underlining of residues. Do not get confused with the application menu-ba. In fact there are two alternative menu-bars which can be distinguished: the one for the 3D-view has a black background, whereas the one for the multiple sequence alignment has a standard white background. The native JMol menu is still available by right-click the JMol pane. It provides all specific JMol functions. Rarely, models vanish from the JMol view. To get them back use the first menu item of the Jmol context menu. It should work on Linux, Windows, Mac and Solaris. It even copes with a fire wall of an intranet (Web proxy). Please enjoy and share your ideas and suggestions. Christoph ------------------------------------------------------------------------------ Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
