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We use JSmol for this course as it 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 Jmol can't and produce a higher quality of output. We list and discuss some of the other packages that will display PDB files below.
We de not require you to use these programs and therefore we do not guarantee 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 version of the JSMol 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. There is an extensive guide to Jmol resources at http://www.umass.edu/microbio/chime/top5.htm#everyone
Swiss PDB 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 probably the market leaded for figures in published papers. It does need a relatively recent machine to run. It has also switched to a commercial distribution for executables so support and installation is not particularly easy.
CCP4 is the UK collaborative computing project number 4: software for macromolecuar crystallography. 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. It is my programme of choice for producing publication quality figures. 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. CCP4mg may be the way to go if you want a more advanced programme than jmol
CHIMERA is another excellent package particularly popular with electron microscopists. It also has a very good feature that convers a structural superposition to a sequence alignment.