Fandom

Scratchpad

MCCE/Tools

< MCCE

215,866pages on
this wiki
Add New Page
Discuss this page0 Share

Ad blocker interference detected!


Wikia is a free-to-use site that makes money from advertising. We have a modified experience for viewers using ad blockers

Wikia is not accessible if you’ve made further modifications. Remove the custom ad blocker rule(s) and the page will load as expected.

A small collection of scripts and tools that might help you using MCCE.

  1. web.site.for.scripts
  2. Create topology files (.tpl)
    • mk_iatom - Creates CONFLIST, NATOM, IATOM, and ATOMNAME from a pdb file.
    • sumup_charge.py - check the overall charge
  3. Improve MCCE calculation
  4. Data Analysis
    • mfe.py - Mean field approximation of residue ionization energy
    • closeup - Measure the distance of each atom to given [x,y,z]
    • res_confs.py - Calculate the RMSD between the specified conformer and other conformers in the same residue
    • getinfo - Guess coupled residues
    • split_conf - Split step2_out.pdb into conformers
    • cmp_yf.py - Subtract two columns from different files (e.g. ionization occupancy output)
  5. Data Visualization
    • mostocc.py - converts step2_out.pdb with the help of fort.38 into a "viewable" pdb file using the most occupied conformers.
  6. Input Data Manipulation
    • addgold - Step2 - addgold.py
    • switchoff - Step3 - switchoff.py
    • zopp - Manipilates energy lookup table energies.opp in working directory

Also on Fandom

Random wikia