Fluctuations plot

[Robert DeLisle]

In other tools, I see plots similar to the fluctuations plots from Bio3D, but the Y-axis is in force units, usually kcal/mol/Ang^2. Does Bio3d allow generation of simiarl plots with force units?

[Xinqiu Yao]

Could you provide a link or reference to what you mentioned similar plots?

[Robert DeLisle]

I misspoke a bit on my request. To be more specific, I'm looking at FlexServe (http://mmb2.pcb.ub.es/FlexServ) and the results contained in one of the structure.#.gauss.hinge files under "Force Constants per residue" can be used to generate a graph of Force Constant per residue. They describe the calculation here: http://mmb2.pcb.ub.es/FlexServ/help/book.php?page=downloadsHelp.php

The calculation of Force Constant doesn't look difficult, but I'm not sure that I have access to all the necessary details through Bio3d.

[Lars Skjærven]

Currently not, but you are welcome to contribute

[Robert DeLisle]

Lars,

I would be happy to write some code to make this calculation. From the description in the paper, it is simply calculating and normalizing distances between residue "particles" which I interpret as individual atoms. This seems easy enough, but the values are averaged over the entire simulation. Do I have access to that type of information in the final aanma results? Any guidance you can give to where I can find the appropriate values would be appreciated.