Thread: Question from NMRWiki Q&A forum Should manipulate PDB file for SPARTA as an input/pred.tab as an input for nmrPipe?
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Unread 11-19-2010, 06:28 PM
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Default Should manipulate PDB file for SPARTA as an input/pred.tab as an input for nmrPipe?
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



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