MACALTop

This program takes an amino acid sequence and calculates the mass of it, like GPMAW can do.

DownloadTop

UsageTop

  1. Start macal.exe
  2. Select the modifications you want to use
  3. Enter the sequence of interest

If you use more than one fixed modifications with the same residues, the first in the list is used. For example, you have the modifications Methylation (C1H2, mass 14.0156500) at DE and then heavy methylation (-H1+C1D3, mass 17.0344750) also at DE and you activate both then only the first (i.e. C1H2) is added to every D and E.

The AAs and modifications characters in the sequence may have different colors:

Blue
A fixed modification has been added to the AA
Green
This is a variable modification
Red
A variable modification which is not activated at the Modifications page and thus has no effect.

At the Composition page you can enter a chemical formula and it will calculate the mass.

CalculationTop

See macal.pdf.

ScreenshotTop

CustomizationTop

All mass values are taken from different INI files. Change these files to fit your needs. If you need the results more precisely then just add some decimals to the AAs and other constructs in these files. You can edit these files with any text editor, like Notepad.

To add, change or remove modifications edit the file mods.ini and then restart the program.

To add, change or remove amino acids edit the file aas.ini and then restart the program.

The format of the configuration files is always the same. Lines starting with ; and empty lines are ignored. Values are separated with a semicolon (;).

aas.ini
File containing amino acids
masses.ini
File containing atomic masses
mods.ini:
File for modifications
term.ini
File containing terminal modifications. The selected modification is added to the respective terminus.

Program settings and options are saved in a file with the name macal.ini located in the users application data directory, e.g. C:\Dokumente und Einstellungen\q002sa\Anwendungsdaten. If you delete this program you should also delete this file.

Command lineTop

macal.exe [options]

options can be:Top

-ini
Change the configuration file. The filename after this switch is used as as configuration file instead of the default.

Example:Top

macal.exe -ini somefile.ini

Build from sourceTop

Get a version of Borland Delphi (at least version 5 with update pack 1), open macal.dpr and click the compile button.

With some modifications you might be able to compile it with Lazarus/Free Pascal. You’ll have to replace the RichEditor with some other editor component.

FAQTop

Q: Why are the results from GPMAW and MACAL different for the same sequence?
A: MACAL has Cystein defined (in aas.ini) as C5H8N2O2S (160.0306492, 160.1967), but GPMAW might use C3H5NOS (103.0091843, 103.1448).