Downloads

Below are the few programs I wrote for solving some specific tasks. It is possible you may find them useful as well. The programs are mostly written in C♯, i.e. you will need .NET framework to execute them. To run the programs, rename the ".dat" files to ".exe".

All the programs are provided without warranty of any kind. They were written to solve my problems, and I am simply making them available. Where possible, I include a source code, so you can modify it to fit your specific needs. If you encounter problems, feel free to contact me, although I cannot promise I will be able to solve them.

PyMOL scripts

empty_remove.py. Removes empty selections (those that do not have coordinate data associated with them). Useful for cleanup if you manually remove structures by picking them with a mouse and typing "remove sele".

join_states.py. Opposite of "split_states" command: create a multi-state object from several single-state ones.

Visualization of XPLOR-NIH NOE restraints in PyMOL

Converts the NOE-like restraints files from XPLOR-NIH format to PyMol pml format. Works for ambiguous NOEs.

Program.

Sample structure.

Sample input.

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Source code.

Phi, Psi angles extractor

Provides a Phi/Psi table for the first chain of the pdb file. If a certain angle is not applicable (termini or missing atom record), values of zero are assigned to both Phi and Psi. Works for NMR ensembles.

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Sample input.

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Source code.

BPS agenda converter

Converts html agenda for the Biophysical Society Meeting from the default Oasis format to a plain text file, containing only essential information. Due to a lack of specific delimeters for affiliations in the html file, some post-conversion editing may be required.

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Sample input.

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Source code.

Peptide synthesizer log file converter

Extracts deprotection values and bar codes from the log files of Applied Biosystems 433A peptide synthesizer.

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Sample input.

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Source code.