VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Tue Jun 17 2014 - 01:17:05 CDT

Hi Luis,

This is an excellent idea! In the same spirit, please allow me to add my own small contribution at https://github.com/tristanc1/torsionplot. It’s an extension/replacement of the Ramachandran plugin, which uses the OpenGL window to plot selected torsions in two or three dimensions as necessary. A little prettier than the old version (with lots of scope for personalisation), and breaks the protein torsions down into the different cases characterised by the Richardson lab (http://kinemage.biochem.duke.edu/databases/rotamer.php). It’s fairly straightforwardly extensible to different torsions as needed – a few lines of code to define each one, and an OpenDX map for the distribution; I’ve included most of the standard glycan torsions, for example, albeit with fairly crappy statistically based maps.

Anyway, it’s not something that’s a key focus of mine – I built it only because I got tired of continually running my structures past MolProbity online, and because I needed a relatively easy way to check my glycans for reasonableness. A lot more that could be done with it... a few examples:

- it currently lists outliers for the chosen case in the TkConsole. This could be built upon to focus the view upon particular outliers and set up an IMD simulation a la the chirality and cispeptide plugins.

- Since the data structure is just a pseudo-molecule with one atom taken from each residue and then moved to its coordinates in phi-psi or phi-psi-omega space, it would be a very simple extension to plot a whole trajectory.

Cheers,

Tristan

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Luis Gracia
Sent: Tuesday, 17 June 2014 12:13 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: rmsdtt, itrajcomp and other plugins open sourced in github


VMD community,

I have moved development of my plugins to GitHub, with a few additional perks. I encourage you to check the latest version and contribute to the open source projects from the following links:

· rmsdtt at https://github.com/luisico/rmsdtt has new iterative fitting functions we’ve used internally over the years

· itrajcomp at https://github.com/luisico/itrajcomp is finally publicly released (though, more documentation on user’s custom functions is still needed)

· clustering at https://github.com/luisico/clustering

· swap at https://github.com/luisico/swap

As I shifted my work away from molecular research so has done my work on these plugins. I’m still maintaining them whenever I find some time, and routinely support lab members and others when requested, but no new features have been added in a long time. I hope that by moving the projects to GitHub the community can pick them up and evolve them in the right direction. GitHub is a great service for open source development. Please, feel free to contribute to the projects, open issues, clone them, hack them, improve them…

Best,
Luis

—

Luis Gracia, PhD
Assistant Technology Engineer
Dept Physiology & Biophysics
Institute for Computational Biomedicine
Software Architect,
Applied Bioinformatics Core Facility

Weill Cornell Medical College
1300 York Avenue, Rm LC-501F
New York, NY 10065
Tel: (212) 746-6963
Fax: (212) 746-6226
luis_at_physbio-tech.net<mailto:luis_at_physbio-tech.net>
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