Contents

MMM individual rotamer PDBs

Contents

This feature has been removed from the EPR toolbox as of version 12.9, due to MMM 2011.2 directly implementing this feature. This page remains for information purposes only. Feature implemented in EPRtoolbox

MMM by default saves calculated rotamers as a rotamer library PDB. This when viewed within PyMOL causes a bit of a problem as you’ve now lost the protein to which the rotamers are supposed to be attached.

Using scripts not distributed with MMM provided by Yevhen Polyhach and Gunnar Jescke, you can make instead make MMM output each rotamer as an individual PDB with the spin label attached to the protein.

WARNING: using this script will fill up your hard drive very quickly For your convenience I’ve created an installation script for the non-standard scripts, which is included in the EPRtoolbox.

This will copy the original MMM files to a backup folder (your_MMM_path/old_files) and then install the new ones. An uninstall script is also included if you wish to restore MMM back to it’s fresh install state.

Now when you select your residues in the Site Scan Window select “No Rotamer Populations” checkbox


This page previously appeared on morganbye.net[^1][^2][^3]

[^1:] http://morganbye.net/mmm-individual-rotamer-pdbs [^2:] http://morganbye.net/eprtoolbox/mmm-individual-rotamer-pdbs) [^3:] http://morganbye.net/uncategorized/2011/04/mmm-individual-rotamer-pdbs