Dimer assignment

[kai xue]

 Hi Lee,

I'm a new user of i-pine auto assignment. I ran into an error message: initial assignment is too unreliable. I am not sure what solution to this error message could be. Is it spectra not aligned good enough? or More peaks need to be picked?

My construct is a dimer in the membrane, I'm wondering if i-pine will be able to recognize there are actually two sets of chemical shifts?

Thanks in advance for your answer and your help.

Regards

Kai

[Lee, Woonghee]

Hi Kai,

 

The message indicates the generated spin system matrix is too sparse to continue the remaining I-PINE assignment processes. It is determined by the number of spin systems and the connectivity between the spin systems. That means 1. You are not providing enough peaks compared to the number of residues, 2. Spin system matrix generation is not good because resonances in different experiments are not aligning well, and/or 3. Established correlation between spin systems are not sufficient. If your protein is a symmetric homodimer and it will have one set of shifts, you should provide only one sequence set and peaks for the set. If they are asymmetric and actually you have two sets, you should provide sequences and peaks for another chain. Probably you can distinguish two chains by arbitrary prolines for running I-PINE. It won’t tell you about dimeric status of your protein. You should be the one who controls.

 

Best,

Woonghee

 

 

 

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

woongh...@ucdenver.edu

 

https://sites.google.com/view/wlee-group

https://poky.clas.ucdenver.edu

https://clas.ucdenver.edu/chemistry/woonghee-lee

 

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

--
You received this message because you are subscribed to the Google Groups "I-PINE/PINE and ssPINE user group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to pinenmr-user-gr...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/pinenmr-user-group/f60287e6-4036-4249-9c84-40fd2a42483an%40googlegroups.com.