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I started the program, then I went to the PoPS Manual Page. When I clicked on the PoPS link again, all my data was lost from the program. How can I get it back?

Every time you click on the PoPS link, a new copy of the program is started. If you want to visit other pages in between using the program, but you want to retain any data you've entered in to the program, then you will need to use the "Back" button in the browser to return to the page which has the copy of the program that contains your data.

In some browsers, however, you may still lose your data.

I wanted to hide buried predictions, but no homologues were listed.

If the expect values of the alignments of the substates are greater than 0.001, PoPS won't display those homologues. Therefore, if no proteins are listed, it means that there is no protein of known three-dimensional structure that is similar enough to your protein to be useful in predicting buried/accessible residues.

I tried to hide buried predictions, but nothing happened.

You must make sure that you have actually clicked on/selected the structure before clicking "ok" (the will be highlighted when it is selected). If you click "ok" without selecting a structure (without a structure being highlighted) then no accessible data can be applied to the substrate.

I created a protease model file in Word, but PoPS won't load it.

The format of any file that is loaded in to PoPS must be text format. If the file is created with a program such as Word, you must ensure that you save the file as text, and not another format such as Word format (*.doc) which is the default format for Word documents, or Rich Text Format (*.rtf), because these files have extra text added to them which will mean that they may not be readable by PoPS.

Questions about the proteome predictions.

How and why are the reasoning tables in the proteome output limited?

Because the proteomes are so large, the processing time and the disk space consumed when trying to predict new targets quickly increases. For example, a request to search the human proteome with a threshold set at the minimum score for the given model will take over 24 hours to process, and use over 1Gb of the server's available processing power. Clearly, when multiple job are running, this cannot be supported. As a consequence, reasoning tables in the output are now limited to a maximum of the top ten sites in a given protein.

Complete reasoning tables can be obtained by using the proteome analysis from a fasta file, or by analysing single proteins in the the standard PoPS program.

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