EPR Toolbox
•

MMM individual rotamer PDBs

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

Older post

cw Normaliser (cwnorm)

Newer post

Peakfinder

Related Posts

In case you missed it

EPR Toolbox
•

EasyRefiner

Faced with fitting well over 30 experiments at room and low temperature at multiple frequencies, as all of my experiments are spin-labelled mutants of the same protein then surely their EPR properties would be similar. I decided that there must be a …

Morgan Bye By Morgan Bye
EPR Toolbox
•

e2af

E2AF or “EPR 2 ASCII folder” is a folder version of E2A, whereby a folder of Bruker EPR files are converted to ASCII data files (readable by any operating system), by default the conversion is to *.csv files (comma separated values). …

Morgan Bye By Morgan Bye
EPR Toolbox
•

Savitzky-Golay - sgol

The Savitzky-Golay smoothing function essentially applies a local polynominal fitting routine to a series of data points to then find the smoothed data points. This has the benefit that for sharp intense peaks (common to EPR) that the line broadening …

Morgan Bye By Morgan Bye
Need some answers?

Frequently asked questions

What distinguishes you from other developers?

I've built data pipelines across 3 continents at petabyte scales, for over 15 years. But the data doesn't matter if we don't solve the human problems first - an AI solution that nobody uses is worthless.

Are the robots going to kill us all?

Not any time soon. At least not in the way that you've got imagined thanks to the Terminator movies. Sure somebody with a DARPA grant is always going to strap a knife/gun/flamethrower on the side of a robot - but just like in Dr.Who - right now, that robot will struggle to even get out of the room, let alone up some stairs.

But AI is going to steal my job, right?

A year ago, the whole world was convinced that AI was going to steal their job. Now, the reality is that most people are thinking 'I wish this POC at work would go a bit faster to scan these PDFs'.

When am I going to get my self-driving car?

Humans are complicated. If we invented driving today - there's NO WAY IN HELL we'd let humans do it. They get distracted. They text their friends. They drink. They make mistakes. But the reality is, all of our streets, cities (and even legal systems) have been built around these limitations. It would be surprisingly easy to build self-driving cars if there were no humans on the road. But today no one wants to take liability. If a self-driving company kills someone, who's responsible? The manufacturer? The insurance company? The software developer?