comment_peaklistΒΆ
usage: comment_peaklist [-h] [--spinID spin_ids] [-i] [-r] [-s]
peaklist comments commented
Comment peaks in an Xeasy or NMRPipe peak list based on a comment file
Comment file format
-------------------
Each line in the file is a peak. Each peak is a list of spin names. Each
spin name should contain three parts: a one-letter code for the amino
acid type or '+' for un-assigned spin systems; an integer residue number
or system number; and finally a dash followed by an atom name. Any of
the three parts can be replaced by a '?' if the part is unavailable. Two
names can be combined into one if the spins form a spin anchor (i.e.
they are a directly attached hydrogen/heavy atom pair). In such a case,
list the residue type and residue number once and combine the atom
names with a slash. If spin anchor names are combined for one peak, they
must be combined for all peaks. You can add or remove peaks to be
commented (comment the comments) with the '#' symbol.
Peak list file types
--------------------
Both NMRPipe .tab files and Xeasy .peaks files are accepted. NMRPipe
.tab files must have been created with the nmrpeaklists library or
otherwise have the assignments in the proper format. The Xeasy format
does not store assignment data. To comment an Xeasy file, you must also
include a spin ID file from CARA. Use the Lua script provided with the
nmrpeaklists library to create the spin ID file.
2D Examples
-----------
G55-H G55-N
+117-H +117-N
or
G55-H/N
+117-H/N
# H84-HA/CA
# F90-HD/CD
3D Examples
-----------
W37-HA W37-CA L87-?
I29-HG2 I29-CG2 Y74-HE
or
W37-HA/CA L87-?
I29-HG2/CG2 Y74-HE
L41-H/N ??-?
S?-H/N D58-C
+132-H/N +132-C-1
# I31-HA/CA Y70-HE
positional arguments:
peaklist input peak list
comments comment file
commented output peak list
optional arguments:
-h, --help show this help message and exit
--spinID spin_ids spin_id file
-i invert the sense of commenting (comment all but...)
-r limit the search to only assigned residues
-s limit the search to only unassigned spin systems