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We recommend Rasmol for this course as it is a long proven package that runs on many operating systems on any computer of the last decade. It has a command line entry which means that with practice you can draw any part of a PDB file the way you want. However more recent packages will do things that rasmol can't and produce a higher quality of output There are many other packages that will display PDB files and we discuss some of them below. There are also an increasing number of Java bases packages such as Jmol and Astex viewer which can be invoked from within web pages without the need to install software other than JAVA which is built into most recent browsers.
We de not require you to use these programs and therefore We do not offer support for these programs as part of the course so if you get into a mess or damage your computer with them that is your problem. Having said that we have used these programs and found them to be good and not give us many problems.
Jmol the java based viewer that we use in the course is also available as a standalone desktop application as an alterative to rasmol. You do need to download software to do this, wheras the applet runs without downloading.
Chime is a plugin for your browser based on Rasmol. However it can be problematic particularly if you want to use Rasmol MIME types. Please read the Rasmol pages before thinking about installing this.
Protein Explorer is a development of Chime using Java to provide extended menu and command window interfaces to Chime . However it can be problematic getting the right browser/PE/Chime combination. Please read the Rasmol pages before thinking about installing this.
Jmol based scripts are steadily replacing CHIME based work. However there are number of good demos of macromolecular structures out there that still require CHIME.
Swiss PDV Viewer is also known as Deep View. It has an interface to a molecular modelling package over the web and a particularly nice way of aligning and viewing multiple protein structures and their sequences. Support and development on this program are diminishing
VMD is a very powerful and pretty package originally designed for viewing molecular dynamics trajectories.
Pymol is increasingly used to produce figures in published papers. It does need a relatively recent machine to run. It is open source but you are encouraged to pay a fee to use it as the author is financed solely through licences.
CCP4 is the UK collaborative computing project number 4. Recently two molecular display programs have emerged from it. CCP4MG is designed to rival pymol and rasmol. It has good molecular superposition and surface and electrostatic display. Coot is more designed for building X-ray crystal structures and displaying electron density. Both are available on a variety of platforms but do require a reasonably high spec machine to run well.