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MCCE Tools
List of miscellaneous tools MCCE offers for your research and convenience. Most of these tools support "-h" flags for additional information and use cases. Some of these tools are intended for pre-run analysis, and some are intended for post-run analysis. Pre...
What is a microstate?
Microstates are
Tautomeric Charge Microstates
All MCCE tools relevant to microstate analysis will start with "ms", like 'ms_top2pdbs" and "ms_hbond_percentages.py". To use any microstate tools, MCCE needs to have the directory "ms_out", produced by "step4.py --ms". Read the steps 1 - 4 tutorial for more...
Koreena and Proton Loading Sites
Gehan and MCCE Microstates
Jose Ortiz-Soto and Photosystem II
How does changing MCCE's parameters change accuracy? (under construction)
MCCE offers a wide range of customizable parameter that influence the accuracy of its pKa predictions. Some major options include varying the internal dielectric constants, numerical Poisson-Boltzmann solvers, Van der Waal functions, conformer sampling level, ...
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MCCE Output Files
As part of the standard four steps, MCCE produces a number of files associated with the initial protein output. These are best understood to be members of six categories: Input: The given PDB file. Often, MCCE programs will symbolically link the name "prot.pd...