Hello,
I am a new user to analysis and have just used the software to assign a
3D data set for a peptide I am working on.
First of all I want to say that after several months of use I am very
impressed with the software, especially with the structure analysis
features. Anyways, as I used it I have noted some bugs / potential
enhancements so I will just list them now. I am currently using V 2.1.2
on Mac OSX with all current upgrades.
Possible Bugs:
1. In peak tab of the quality reports, every single peak from my HNCO
spectrum is flagged with 'Impossible bond 57 LysC-58GlyN' etc... This
experiment has been set to HNCO, so I doubt this is the problem. As far
as I can tell, this is a perfectly normal connection and is being
improperly flagged, although I may be wrong.
2. This problem is a bit more of an enigma. During my initial assignment
I set some protons to be the HD1 proton of histidine. I then created
distance restraint lists from the NOE data. Later I realized, that the
HD1 proton was actually the HD2 proton, so I renamed the appropriate
resonances, which were then correctly updated in the restraint lists.
The problem is that when I export the restraint list, it is exported as
the initial HD1 instead of HD2. Also, if I analyze violations a pdb
file, the software looks for a HD1 atom instead of the HD2 atom which
the restrain list shows.
3. Every once in a while if I am assigning a peak and then decide to
delete it, the assignment panel will mess up. This isn't really a
problem, and I have not been able to reproduce it, but I just thought I
would let you know.
Possible enhancements (I realize that you are not working on
enhancements right now, but maybe in the future):
1. In the resonances tab of the quality reports, some resonances are
flagged because one of their peaks have a large delta. However, when I
click show peaks it can be tedious to find out which peak exactly is the
problem. Would it be possible to include a setting to pull up the
violating peak or at least highlight it?
2. In the format converter would it be possible to include support for
Xplor when exporting distance restraints. I am currently using the cns
export, which works well because it is simple to modify the output files
into xplor format. It is not terribly important, but it would be nice.
Similar to this theme, it would be nice to be able to export a sequence
list in xplor format.
Finally I have one question:
Some of my resonances are flagged in the quality report because they
have multiple bound partners. Say a glycine Ha bound to both a Ca and a
Cb. I understand how this is a problem, but I have not found a way to
fix it. I am not sure where this error is coming from, since in some
cases there are not any peaks which connect a resonance to the improper
bound partner.
This is a bit of a list to send you, but I figured that I would give all
my suggestions at once. Overall though I am impressed with the software
and especially the active support/development. If you need a project
file or more detail please let me know.
David Langelaan
Dalhousie University
|