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In the development of GPMAW a new compiler was used, which necessitated the conversion of all string handling to unicode strings. This necessitated that a large part of the program had to be rewritten, which has seen several internal changes, and a bug or two may surface in seldom used parts of the program - these will course be fixed as soon as possible. Another aspect is the size of the program has doubled, but this has no influence on the speed of the program. Corrections leading to 9.01 see at bottom.
The most visible change in the new version is a new menu interface that allows for a changing the color scheme and more changes in layout. More commands has also found their way into the toolbar.
The color scheme may be changed by selecting the down arrow next to the help button.
The painting of peptides has been expanded with painting of cys-linked peptides.
Continuing with the cystines, you can now save and load the disulfide linkage pattern of a given protein. This saves a file containing cys1 to cys5, cys2 to cys4 etc. and can be very useful if you have multiple proteins with the same pattern, but may differ in sequence.
The cysteine cross-link editor now also works with a table combined with direct coloring and clicking on the relevant residues in the sequence (you can still edit numbers directly).
Stability / Aggregation propensity. A new graphical interface for the TANGO program and an alternative list of protein parameters. This window is called from the pop-up menu in a sequence window.
A large number of minor updates has been carried out in the program. Among these are:
- Search in alignment.
- Extra interline spacing in the sequence window. Also an option in Setup.
- In the setup you can set the default behavior of the 'Enable all residues' in the Edit sequence window.
- The Open dialog has been enhanced with more information available when selecting a new sequence.
- The MRU list (Most Recently Used files) has been extended to 9 files.
- The Charge vs. pH window has been spruced up a bit with more information.
- You may now copy the intact mass in 2/4 digit precision from the drop-down menu in the sequence window.
- You can now call the coverage map window from the ms search results.
- The coverage maps has seen small improvements, in particular all the windows now support printing (MS search coverage, ms/ms coverage, cleavage)
- A few extra parameters and an updated X! Tandem search engine for ms/ms searching.
- Corrections made in 9.01 / 9.02.
- Ctrl+F now works for copying a sequence to clipboard in FastA format.
- When copying the protein list to clipboard in the ms/ms search, HTML tags were included. These have now been removed.
- In ms/ms search the ‘Point mutation’ option was linked to the ‘Semi cleavage’ option. These have now been separated and work independently. The point mutations are now shown in the details box (top line) when the relevant peptide has been selected. A small graph has been included in the top of the peptide details window to show the relative total ion intensity of the selected ms/ms spectrum (showing from lowest observed to max observed ion intensity). HTML tags removed when copying to clipboard.
- New ‘Upgrade info box’ easier to read and does away with a dialog box.
- A number of calls to external programs did not work. Is now fixed. In particular call to BLAST was non-functional. A new version of the NCBI BLAST has been included in the upgrade.
- Retrieval of sequenced from indexed FastA databases is now fixed.
- The number of display options has been increased.
- Calling glycosylation commands from the sequence window fixed.
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