A new release of Wordom is quite near. It wil be released in the new website (http://wordom.sf.net) which is right now under construction
Molecular simulation analysis and manipulation
Wordom is a (simple) command line utility conceived to spare the user some time in manipulating and converting dcd, xtc, pdb, crd and xyz files. Wordom is also a versatile program for a broad range of types of analysis of molecular dynamics trajectories. Original tools in Wordom include a module for the calculation of order parameters to monitor polypeptide aggregation and a procedure to evaluate significance of sampling for principal component analysis. As a plus, it's easy to use in shell scripts. Due to its simplicity, it is very easy and straightforward to add your own analysis module. Basically, all you have to do is write the algorithm. The data are made available by the existing wordom i/o modules.
Wordom is free software under the GPL license.
If you use wordom in your work please acknowledge it using the following reference (see it on pubmed ):
M. Seeber, M. Cecchini, F. Rao, G. Settanni and A. Caflisch; |
- along with any paper which might be relevant to the module/algorithm that you are using (see documentation)
Flash News |
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v.0.21(_rc6) is out! go get your copy |
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v.0.21(_rc5) is out! go get your copy |
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v.0.21(_rc1) is out! go get your copy |
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-ocrd badly writes 4-letters resname in output crd files (only three letters are displayed) - FIXED |
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Due to memory allocation problems, Quality Threshold clustering was broken. Please download version 0.20d-2 for a fix. Hierarchical clustering works almost correctly, with possible cluster number mixup regarding the isolated frames cluster(which might uncorrectly appaer NOT as cluster number 0) - work still in progress - FIXED |
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