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How to change reference data in Reference Chemical Shifts window? - Printable Version

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How to change reference data in Reference Chemical Shifts window? - MikaelK - 09-08-2019

At the CCPN Conference workshop we had a short discussion about how to use different chemical shift reference data in Analysis V3’s Reference Chemical Shift window (Molecules > Reference Chemical Shifts). Different reference data can be useful for example for intrinsically disordered proteins which have slightly different chemical shifts than folded proteins.
 
At workshop, no one remembered exactly how this was done. We decided that someone from CCPN would check this and write it to forum. So, can someone from CCPN write how reference data is changed? (file location, file format, what else one needs to know?)


RE: How to change reference data in Reference Chemical Shifts window? - LucaM - 09-18-2019

Hi Mikael, thank you for your request. At the moment is probably not easily doable. We are discussing a simplified way to achieve this and allow users to add their own references. This will involve changing the GUI for the module as it is now.
May I ask you to share one example you wish to load in? Or in which format do you have, eg. csv, hdf5, Bruker... ?
Thanks


RE: How to change reference data in Reference Chemical Shifts window? - MikaelK - 09-19-2019

My colleague told me an example how she would like to use it:

IDPs (intrinsically disordered proteins) won't fold and for this reason folding isn't really affecting their atoms' shielding. Neighboring amino acids are the main source for shielding. Therefore, if someone wants reference chemical shifts for an IPD, they need to be calculated every time from the IPD's sequence. In other words, one needs to calculate sequence-specific random coil chemical shifts for the IDP. Here is one website which can do this:

https://st-protein02.chem.au.dk/ncIDP/

They are other programs, servers, etc. to do the same thing. The one in the link is the best one. The input file for Analysis, should be output file from this program ncIDP? I am not sure what format ncIDP is using. Could it be ShiftX format? You can make an example output file by making own short sequence (you can just type it) and then running it.

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RE: How to change reference data in Reference Chemical Shifts window? - VickyH - 09-19-2019

Yes, that's really helpful, Mikael. Many thanks.
We'll be able to take that into consideration as we re-design the referencing info module.
Vicky