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The7.01 upgrade of GPMAW brings the following changes.
Cleavage analysis: A problem with saving the cleavage analysis as a coverage file for later incorporation into the 'Coverage analysis' window has been fixed. You can now also have labels in the peptide bars.
Alternate mass file in the peptide window has been corrected. Previously it did not load a new mass file.
Peptide mass search: When pasting a new mass list into the table, the datafile input line was not changed to reflect this.
Edit modification file: The format of Unimod xml file (www.unimod.org) has changed, so users trying to upgrade to a new file got a non-functioning Unimod file. Version 7.01 can read both the old and the new file format.
Fragment analysis: Doubleclick on a 'difference mass' generated multiple transfers - fixed.
Web retrieval: A problem with using accession numbers has been fixed - if you have problems in the Web Entrez Search, use GenPept format instead of FastA. Default is now GenPept. A minor problem with extra text during the transfer has been fixed.
Clear coloring only worked for the top window - fixed.
A problem when reading FastA files from disk has been fixed.
Cleavage analysis and Coverage analysis now have smooth-working scrollbars.
Working with Cysteine residues (Cys): When the selected mass file has a Cys mass value of 102 or 103, GPMAW defaults to all Cys residues having a mass of 102 when the SS button shows SS and mass 103 (reduced) when the button shows SH, thus allowing a quick switch between oxidized and reduced Cys. If Cys cross-links have been defined, they will be shown as red lines when oxidized Cys and gray lines when reduced.
From version 7.01 you can now 'modify' Cys to be always reduced - define a modification of H1 for composition and a name like 'Red.Cys'. In the 'Simple modifications' (right-click on residue or double-click for modification dialog) you can now select a 'Reduced Cys' with this effect. The effect is that when Cys is modified it will not be affected by the status of the SS button (works for any individual modification of Cys).
A new Absorbance scale has been added to the calculation of the absorption coefficient. The values of Pace et al (1995) should be more accurate than the old values of Gill and von Hippel. You can find a discussion on this here http://www.expasy.org/tools/protparam-doc.html.
Pace, C.N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 11, 2411-2423. [PubMed: 8563639]
Gill, S.C. and von Hippel, P.H. (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182:319-326(1989). [PubMed: 2610349]
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