Dear Charles and xplor-nih users, Please skip the previous message titled with " protein and dna docking with PRE" which was not completed. Sorry the inconvenience.
As I only have PRE data for the protein/dna complex without any intermolecular NOE constraints, the results from "newRefine.py" are not good in which the input complex structure was modeled manually. After searching the mailing list, Charles suggested in a message that the calculation should be better started based on the /eginput/diffTens/dock.py. I modified the dock.py and replaced the diffPot with prePot (the chemical shift perturbation was not included). The script worked, but there two problems: 1) the protein structures were disrupted in all the output structures. 2) there is a relative orientation between protein and dna in the output, but they do not have direct contact. I'm not sure the problem is coming from the experimental data or something wrong in my modified script. Would you please give any suggestions to solve them ? Attached is the modified script. Thanks. Best Changdong
dock_pre.py
Description: application/chimera
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