XEASY organizes the assignment of peaklists in the following way:
An "assigned" peak list provides the relation between peak position in a spectrum and a resonance numbers ("proton number") in all dimensions.
A "proton list" (*.prot) translates this resonance number into an atom name (HN, N, HA, HB2, CA, ...) and a fragment or residue number.
A sequence list (*.seq) resolves the type of residue from the the fragment number.
If a fragment is mapped to a different place in the sequence (i.e. from pseudofragment 300 to residue 9), the fragment number in the proton list is changed. Fragment 9 should not exist in the sequence before (If it exists, all atoms that are defined in both fragments are duplicated). The change of fragment type is done independent of mapping, by changing the "Fragment" entry in the edit window. All atoms that are defined in the library for the new fragment type are added to the proton list, if they are not already there. Again, all existing assignment numbers stay the same. This mapping scheme works only if the resource "XEasy.new_atom_numbers: false".
With this scheme you never change assignment numbers in the peaklist, so that a peaklist which you created and assigned in the very beginning should still be in agreement with a proton list where fragment types and mapping numbers were changed. On the other hand, you have two problems:
SPSCAN has a completely different mapping scheme: it changes assignment numbers in the peaklists to achieve mapping. Doing this, it checks whether the resonances really exist in the library, and it adapts the atom names if necessary. You can get fragment number and atom name from the assignment number, i.e. you dont need a proton list (except in mode 5). It will be confusing to mix both schemes. Either you use XEasy.new_atom_numbers: false and do all mapping in XEASY, or you use XEasy.new_atom_numbers: true and do all mapping in SPSCAN.
SPSCAN supports several different assignment modes, but they can all be read correctly by XEASY. To load XEASY-generatedpeaklists into SPSCAN, use assignment mode 5. SPSCAN supports following assignment modes:
#ASSIGN_MODE 5 <proton list> <sequence list> <residue name>in the peak list header tells SPSCAN to load the correct *.prot and *.seq files. (XEASY does not care about this line - each time you change the list with XEASY it is lost. You have to re-introduce this line or use "assign"/"get assignment".)
You can adapt any peaklist to your favourite XEASY proton list with Integration: "assign"/"reassign".
You can also check whether peaks are assigned to resonances that do not exist (e.g CB of GLY), and whether use of pseudoatoms is consistent.
Mapping of residues:
The mapping scheme in SPSCAN is different from mapping in XEASY. SPSCAN changes assignment numbers and checks whether the atom name exists in the new fragment type. XEASY does not change numbers, and it does not detect a problem, if some atom names may become invalid. It simply adds those atoms to the proton list that have a library entry for the new residue type, and that are not in the current proton list.
xeasy_striplist fwd <;nr_prev>; <;nr_next>; <;spectrum1>; <;peaklist1>; <;spectrum2>; <;peaklist2>; ...
xeasy_striplist bwd <;nr_prev>; <;nr_next>; <;spectrum1>; <;peaklist1>; <;spectrum2>; <;peaklist2>; ...
Writes for each residue a sorted striplist of probable sequential neighbours. "fwd" gives you the possible sequential neighbours at n+1 position, bwd at n-1.
nr_prev and nr_next are the number of spectra for which a strip is to be displayed for the N-terminal and C-terminal fragment of a possible sequential connection. The following arguments are nr_prev spectrum/peaklist pairs and nr_next spectrum/peaklist pairs.
spectrum1... are names of spectra_path/spectrum.3D.param files without path and ".3D.param". peaklist1... are peaks_path/peaklist.peaks files (again without path and extension) which are assigned in spscan style, and which match the spectra in their order of dimensions. I.e. w1 of the spectrum must be the first dimension of the peaklist. If your peaklists are written from a spectrum that was not loaded in orientation "1 2 3", they are in a different permutation: load the spectrum as "1 2 3", load the peaklist (if your peaklist does not have linewidths, set some default linewidth with "modify pl"/"check linewidth"; if your peaklist does not have assignments set "assign"/"get assignments"), write the peaklist out.
To check the sequential connections in XEASY, load all spectra in the correct orientation for strip display. Load the peaklists that you want to see displayed with the spectra. (The peaklist that you give in the spscan command is not automatically displayed by XEASY, it is only used to define the position of the strips.) With "es", "sl" load the striplist for the residue you want to check. Display with "gs", starting with strip 1.
The "spectrum" names are not checked by the macro, i.e. they dont have to exist when the striplists are created; XEASY has to identify the spectrum under that name. The "peaklist" names are normal SPSCAN names, i.e. they can have a full pathname, or they can be project id names. The peaklists do'not have to exist when the strips are evaluated in XEASY.