Dynamic Network Analysis Issue

[vibhor agrawal]

Hello all: I have a question regarding the protein network.I have a protein network created using the Network View plugin of VMD.OI want to carry out the correlation based network analysis on that network.I want to perturb the network by removing some nodes and analyzing the impact in the Centrality and betweenness etc.I saw in documentation following mentioned tutorial: Introduction to correlation network analysis with Bio3D I wan't able to find this documentation in the package manual and ways If i can import the dcd,pdb,cij and other files from the Network View plugins generated files. Please help. Thanks Vibhor

[Lars Skjærven]

Hi Vibhor, Thanks for you interest in bio3d. The vignette (and related functions) for correlation network analysis is under development and therefore only available through this repository (see branch feature-cna - if I'm not mistaken). You can check out the "Wiki" on how to download the development version (e.g. through git). You can certainly use bio3d to read dcd and pdb files, and the correlation file obtained from VMD I assume you can read in to R with read.table or related functions.

The "Issues" page (where you just submitted) is for bug-reports and suggestions only. Since your post is not a "bug" I will close it. But please send us an e-mail if you have further questions on the usage of bio3d.