Frequently Asked Questions

If your question is not on this list, please email the webmaster.

Monster needs Java version 1.4.1 in order to run properly. You can download Java from here. Be sure to close your browser and relaunch it after installation is complete.

Monster has a time-check built in, it is generally assumed that if your job has taken more than 15 minutes, and no result files have been found, then Monster has failed to finish its job. You will be told, upon submitting a job id, whether or not this is the case.
If you have recieved an error message saying that monster has failed, then there IS a problem with your submission. Please send an e-mail to the webmaster with the job ID. Note, if you are submitting your own version of an atomic coordinate file, that Monster assumes strict compliance with the PDB format. The official PDB format can be found here.

Changes in residue ranges are not allowed for the original chains in the atomic coordinate file. For example, if there were four chains A, B, C, and D, you cannot make changes in the residue ranges for any of these chains. However, you can copy the original chains to new chains (e.g. copying chain A to chain E in the example above) and make changes to the residue ranges in the new chains.
A residue range for a chain cannot be changed if the 'ignore' checkbox is checked for that chain. This is the default when creating a new chain, so be sure to uncheck this checkbox.

4. Why dont I get the correct residue ranges in the chain pairs tab in the parser?

Changes to the residue ranges can be made by double clicking on the residue field, typing in the new number, and hitting "Enter". The last step is important - failure to do so will retain the original numbering.

You need to first choose the pair(s) of chains you wish to analyze before running a job. You will need to press the "choose pairs" button, and check the relevant chain pairs in the "Chain Pairs" tab that appears.

The contact surface area is calculated using MSMS. In the rare instances that MSMS has a segmentation fault, the result shown will be '0.0'.

7. Why does my contact surface area for certain residues, in the 2D Bonds viewer, show '0.0'?

The contact surface area is calculated using MSMS. This may either mean that MSMS had a segmentation fault (see question 6) or the residue simply was not close enough, and therefore did not have any contact with other residues.

8. Why does the total contact surface area listed in the results page not match the total contact surface area calculated in the Bonds Viewer?

The reason is that the total contact surface area on the results page, is taken directly from the MSMS analysis file, and is the true total surface contact area for that chain.
However, the total contact surface area calculated for each chain in the Bonds Viewer, finds the sum of contact surface area of all the corresponding atoms in the results.
Not ALL the atoms that are involved in the contact surface, are deemed to form bonds, and do not make it into the results. This lowers the contact surface area total in the Bonds Viewer.

9. Why do I get a long error list/stack dump when I press the '2D BONDS' button to load the viewer?

The session for the job ID is timed out after 30 minutes of inactivity.
This is simply solved by pressing the reload/refresh button, or by re-entering your job id and pressing submit.

10. Why did my some of my residues disappear?/How do I make certain residues disappear?

If a menu option, or a slider, was used to change the view and a residue either no longer has any bonds showing, or is not present in a model, the residue itself will disappear. The display automatically rearranges the remaining residues to fill the space available.
In addition, there is a feature in the 2D Bonds view, implemented to help users better create the view they would like to see, where if a user selects one or more residues, and chooses the 'Hide Selected Residues' option in the 'View' menu, the residues will disappear.

11. How do I bring back the residues that disappeared?/What do the various 'Edit->reset' options mean?

To reset 'all' means the viewer is restored to the state it first appeared in, where every bond, and every residue is seen, and the sliders are at their default positions.
To reset 'sliders' means the sliders are returned to their default positions, and bonds (and corresponding residues) are restored. The restored bonds however still correspond to the bond types turned on or off in the 'View->Show Bonds' menu.

To reset 'layout' means to only restore the colors, and the shown bond types to their defaults. The restored bonds still correspond to the slider positions.

Each number on this slider corresponds to the minimal number (the cut-off) of models every bond is present in. Therefore, at 15, the viewer will only show all the bonds that are present in 15 or more models. This was implemented to enable a user to see how 'common' some bonds are.

13. Why does the 'Models Cutoff' or the consensus file never show bonds that exist in less than half the models?

Each model has a number of bonds unique to either that model alone, or to a few of them. There are a large number of these, and they are deemed irrelevant and ignored.
This was also important because showing all these bonds and residues rendered the display unreadable/unmanagable.

A ".java.policy" file needs to be saved in your home directory, granting write access to the 2D Bonds viewer. A recommended ".java.policy" file can be found here.
It is important that not only do you type the file name in full when saving it, ".java.policy" (with the '.' prefix), but you should enclose the file name in double quotes.
Directions for saving the .java.policy file varies from *nix to Windows:

Linux: It must be saved in your /home/user directory.
IRIX/SGI: It must be saved in your /usr/people/user directory.
Windows 2000: It must be saved in your C:\Documents and Settings\user directory.