Here you are.
Rasmus Fogh wrote:
> Dear David,
>
> Thanks for the nice words, and for taking the trouble of reporting
> your bugs. I think it would be easier for us to get hold of problems
> 1) and 2) if we had your project to look at. Would it be possible for
> you to tar it up and send it to us?
>
> The question about Glycine Ha bound to Ca and Cb sounds puzzling. That
> error message ought to mean that the resonance was indeed bound to the
> wrong atom some of the time. The only things tha spring to mind would
> be mutliply assigned peaks, confusion between HAa and HAb, or
> something seriously messed up in the data. I guess we can see that one
> too if you send us the project.
>
> YOurs,
>
> Rasmus
>
> ---------------------------------------------------------------------------
>
> Dr. Rasmus H. Fogh Email: [log in to unmask]
> Dept. of Biochemistry, University of Cambridge,
> 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
>
> On Tue, 2 Feb 2010, David Langelaan wrote:
>
>> 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
>>
>
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