[Question from NMRWiki Q&A forum] Should manipulate PDB file for SPARTA as an input/pred.tab as an input for nmrPipe?

[nmrlearner]

Should manipulate PDB file for SPARTA as an input/pred.tab as an input for nmrPipe?

HELLO,I have a PDB file of two chains A and B, but as it mentioned in the manual of SPARTA, it read only one chain and the second chain will be ignored. I tried it and it did so. The PDB file I have was the output from Modeling of chain A (that had a mutation). I had refined the modeled structure after docking it into chain B (native). After refinement I have a PDB file of two chains. Now, I have two solutions in mind to get chemical shift prediction plotted in a spectra but I do not know if any of these can be a correct strategy:1- In the PDB file, change chain B to chain A and change the numbering so that it continues after chain A.

OR

2- In pred.tab file for chain A, add pred.tab data from chain B; and don't forget to change the residue number and SEQUENCE DATA to the new file made.

Is there any other solution?

Thanks in advance,

Mahnaz



Check if somebody has answered this question on NMRWiki QA forum