Print

Print


Dear colleagues,

I've been experiencing some issues trying to assign leucine side chains in my protein using CCPNMR Analysis 2.4.2. More specifically, I cannot assign Hda and Hdb to their respective Cda and Cdb. I'm able to assign the carbon atoms but when try to add their respective hydrogens I see the software somehow "updates" all the resonances (already assigned) and makes a real mess to be fixed. 

It seems that analysis assigns the carbons types to Cd2/Cd1 or Cd1/Cd2 before assigning them to Cdb and Cda. That is fine. The same does not seem to happen to the hydrogens, it seems to consider only Hd2/Hd1 or Hd1/Hd2 atom types for both Hda and Hdb. I’ve  also noticed that Analysis assigns each atom type according to the their shift values; i.e. Cda will be the carbon with lower value and Cbd with higher value. This is fine. The problem starts when Hdb has a lower shift value than Hda. The software ends up connecting Cdb to Hda instead of Cdb to Hdb. This issue happened with all leucines (and probably will with valines, haven't checked yet) in my protein; it turned out that the Cda (with lower shift value) cannot live together with their respective high shift value Hda, because the software identifies that delta "a" atoms (both Cda and Hda) should only have the lower shift values, thus renaming everything, and stressing me of course. 

Has anyone experienced the same or similar problem? Any recommendation or solution? It'd be nice (and useful) if there is a "switch off" button somewhere for this.
Thank you very much for your answers and comments.
Best,

Germán Sgro


--
Dr. Germán Sgro

Departamento de Bioquímica
Instituto de Química
Av. Prof. Lineu Prestes, 748
Cidade Universitária
São Paulo - SP
Brasil
05508-000
T:+55(11)3091-3312
ORCiD: 0000-0002-2831-7945
Website do Instituto: http://www3.iq.usp.br/