Hey Ed,
This email address is being provided to me by Sebastien Morin.
I am a new user to RELAX software and currently trying to use it for model free analysis in the GUI mode. i thought of asking you as you might have encountered the following problem:
The situation:
I have experimental data for R1, R2 and NOE at two fields (600 MHz and 800 MHz) on a large protein kinase. As expected, i do not have data for all the residues in the protein sequence. on searching through Web, i have found a X-ray structure, which also have some parts missing, possibly due to poor electron density in those regions. I learnt from RELAX that one can create spin system solely based on sequence and then attach protons to it or by using a pdb structure. For model free analysis possibly, i would need a pdb structure (not entirely sure!); as i can see, an example in the manual illustrating without the use of the structure (page 103)
The problem:
When i tried doing it by creating spin systems using amino acid sequence alone, the system never got executed. However, when i started doing it with structure as an input., it did run but then gave me an error message for all the spins as follows:
for spins with all six data parameters:
spin YYY deselected due to absence of any relaxation mechanisms
and for spins with no data:
spin YYY deselected due to absence of any data.
the second one is understandable but not sure about the first one .
To check whether something is wrong with the complete data sets,
i created new data files for only first two residues with structural coordinates extracted for these two residues. In this case, the program worked well.
Questions from me:
1) Does that mean the absence of data for certain spins, loaded either from sequence or structure, causes this problem?
2) Can i do the whole analysis just by using the sequence.
3) Does the software actually need minimum six values (R1, R2 and NOE at two fields) for this analysis or it can work with >= 3 values? As for some residues, i have < 6 data values. I am currently ignoring those residues with < 6 data values as i wasn't sure if model free analysis would be able to handle that.
4) I am still unclear with the initialization of diffusion tensor. In the GUI mode the first row asks for The diffusion tensor parameters:
I have tried to understand what is written in the manual, but i am not sure if i understood it correctly.
Would you be able to guide/suggest me on this. Any suggestions from your end is highly appreciated.
Many thanks and regards
Nav
Missing data for spin system and compatibility in GUI