Recipe for setup
This is a step-by-step recipe on how to set up ANSIG for a
project. Parts of this depend on whether the project involves
homonuclear 2D spectra only, or heteronuclear 3D/4D spectra.
Control file
Copy a control file from one of the
examples, rename and edit it to fit your project.
- The items with the comment general usually do not
need to be changed, while the items with specific usually do.
- The dictionary file is a
special case. There are three different versions of the dictionary in
the
ansig/lib directory:
- The crosspeak file and its backup should not exist when one
starts a project; ANSIG will create them with the given names.
Sequence file
Copy a sequence file from the
examples, rename and edit it to put in your sequence. Note that the
residue type names (Ser, Ala, Trp,...) must match the names in the
dictionary. The name comparison is case-sensitive; Trp is not the same
as TRP. The residue numbers (=names) can be at most 4 characters
long. They do not have to be integers; letters are also allowed.
Spectrum description file
Copy a spectrum description
file (spd file) from one of the examples. Choose the spd file from
pgc2 if you have only 2D homonuclear spectra, or maybe also 15N-edited
3D spectra. For 3D and 4D heteronuclear spectra, the ras example spd
file is probably more helpful.
It may be a good idea for a beginner to try to set things up only for
one or two spectra to start with, in order to become familiar with the
ANSIG program. The full set of spectra can be added later. Note that
the if you are going to start picking crosspeaks, then give the
spectra sensible names from the very start, since it is difficult to
change spectrum names later.
Spectrum matrices
The spectrum matrices must be in ANSIG format (which is the same as
Azara format). Use the various
conversion programs
available to reformat your spectrum matrices, if necessary.
If there is no conversion program for the specific conversion you
need, then it must be written. Either one can start from the source
code for the existing conversion programs to help create one's
own program, or one writes a program to produce an intermediate file
of the spectrum matrices in a so-called serial file (the simplest
possible format), for which there is a conversion program in the
distribution. Of course, this requires that one knows the format of
the matrices that need to be converted.
The chemical shift referencing of spectra should be done by filling in
the appropriate values in the spectrum matrix parameter files produced
by the conversion programs.
Initialization file
Copy an initialization file
from one of the examples. Choose the appropritate one based on which
spd file you chose in the previous step.
There is no harm in keeping all the macro and AL procedure definitions
in the initialization file, even if you will not use them; the space
they occupy does not affect the rest of the ANSIG program. It is
always easy to remove such definitions from the initialization file at
a later stage.
Per Kraulis 10 Apr 1996.