Hi,
I have been using analysis (1.0, 2.0.7 and recently 2.1.0) for past two
months in combination with Aria to solve a protein-peptide complex.
For all my previous structures, the strategy I used to use is assignments
using CARA and then picking the NOESY peaks using PIPP (manually!!!) and
then (in some cases) using KNOWNOE from Auremol to improve the assignments
I have few questions regarding analysis:
1)I have almost 90% complete chemical shift table (in CYANA format,
generated by CARA). I import it to analysis using format converter which
does a decent job except for Val and Leu residues. The methyl groups
(CD1,CD2,CG1,CG2) are imported non- stereospecifically , thus when I create
synthetic peak list, analysis will create the peaks for all combinations
(eg: CD1 will be paired with both HD1 and HD2). Is there a way around this ?
2) All my spectra are calibrated for my chemical shift table, however when
analysis will create a synthetic peak list, it moves the shifts around.
Although there are no huge differences , I would like to have a fixed
chemical shift table ( as in case of PIPP or CARA, both the softwares will
not change the shifts unless and until I want to change them). Is there some
way where the shifts will be fixed and synthetic peak list will be generated
based upon that fixed set of resonances?
3) While generating a synthetic peak list for NOESY spectra, can I specify
in advance the threshold for the particular spectrum ( for example in
Auremol, the software will calculate the threshold either automatically or
manually, and pick the peaks above this threshold)?
4) While generating the synthetic peak list (say based on the structure) lot
of peaks are picked multiple times, is there a simple way to remove the
duplicate peaks or merge them?
Thanks in advance,
Regards,
Lalit Deshmukh
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