Some of Webmol's functions such as changing color fails with Java version 1.4.2 and some sub-versions of Java 1.4.1 (eg Java 1.4.1_06)
MSMS has been known to cause a segmentation fault, rarely, on some pdb files, leading to a lack of contact surface area. (Please see FAQ).
Monster & HBplus:
Both Monster and HBplus are unable to assign a parent heavy atom to a proton, if the proton appears BEFORE the heavy atom in the PDB file.
The common example is that of terminal protons found at the beginning of the first residue, rather than after the last heavy atom in the same residue.
Mac & Java:
For some reason, the only browser on the Mac OS X platform that seems to run any applets is the OS X native Safari browser. Attempts to get any applets working in other browsers has failed.
Some PDB or result files are so large (eg 1KYO) that they may cause an 'out of memory' error when loading into an applet.
Three options available are:
Reload the browser and make sure no other pages are open.
Close all other programs.
Use a computer that has more RAM.
In Java 2, Sun introduced a new system property called 'entityExpansionLimit'. This limit enabled a developer to strictly control the number of entities parsed in an XML file. However, in some versions of java, below 1.4.2, this limit is set by default, and prevents the applet from loading a large XML results file. The best two solutions are:
Install the latest version of java, at least version 1.4.2
Add these lines to the '.java.policy' file (download here. See FAQ for directions.):