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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 >