Re: [gmx-users] g_cluster analysis for structure refirement

Thanks! That was very usefull. BTW have someone tried some software for visualization of such clusters and compution of the percents of the SS elements in each cluster (for instance by comparison of the most representative structures from each cluster etc). Might this VMD plugin

Re: [gmx-users] g_cluster analysis for structure refirement

Hi Tsjerk, thanks for suggestions! Some additional questions regarding g_cluster method. 1- how most correctly select cutoff value for clustering of the surface-exposed loops assuming big number of clusters? In literature I've found cutoff ~ 1.3 A for enzymes active-site loops applicable for

[gmx-users] g_cluster analysis for structure refirement

Dear Gromacs users! I'd like to use g_cluster utility to cluster a big set of models produced by Modeller as the result of the refirement of some parts of my protein. In this case all structures differs only in the conformation of 1 longest loop (~ 30 amino acids including 2 disulphide bridges)

Re: [gmx-users] g_cluster analysis for structure refirement

Hi James, The first part is just conformational clustering, for which you can use g_cluster. The easiest is then to collect the structures belonging to the different clusters in different files (which g_cluster can do), which you process separately to extract those properties you're interested