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GunnerLab / Stable-MCCE

Stable version of MCCE.
MIT License
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A quick question about bkn contribution to the calculated Em #177

Closed ghost closed 3 years ago

ghost commented 3 years ago

In my study, I need to know what factors led to the calculated Em potential of the cofactor in the study. I performed the MFE.py analysis, and I intersted to breakdown the backbone contribution to see which residues are contributing to this term.

I dont know how to that, could you help ? Is there any tool available for this .. thanks

newbooks commented 3 years ago

Here is a description of mfe.py command: https://gunnerlab.github.io/Stable-MCCE/tools/#mfepy

To analyze the contributing factors at Em, you will need to run a Eh titration that covers the midpoint. If the midpoint is out of titration range, you can choose a Eh/pH point.

Examples (residue ID is from pK.out file): mfe.py HEM+A0105 # do mfe analysis at midpoint mfe.py HEM+A0105 -c 0.1 # do mfe with pairwise interaction display cut off at 0.1 ph unit mfe.py HEM+A0105_ -p 200 # do mfe at Eh 200 mV