issue regarding cmap function

[santosh chaudhary]

I want to calculate protein network which include all heavy atoms. I have found a relevant post related to this issue (https://bitbucket.org/Grantlab/bio3d/issues/162/q-a-question-about-bio3d-cna ) and i followed following steps to calculate the network and node betweenness.

inds_1_chA <- atom.select(pdb1.1, "noh")
trj_1_chA <- fit.xyz(fixed = pdb1.1$xyz, mobile = dcd1.1,  fixed.inds = inds_1_chA$xyz, mobile.inds = inds_1_chA$xyz)
cij_1_chA <- dccm(trj_1_chA[, inds_1_chA$xyz], grpby=pdb1.1$atom[inds_1_chA$atom, "resno"])
cm_1_chA <- cmap(trj_1_chA[, inds_1_chA$xyz], grpby=pdb1.1$atom[inds_1_chA$atom, "resno"], dcut=4.5, scut=0, pcut=0.75, mask.lower=FALSE, ncore=8)
net.cut_1_chA <- cna(cij_1_chA, cutoff.cij=0.50, cm_1_chA = cm_1_chA, ncore = 8)
plot(net.cut_1_chA, pdb1.1)

The issue is regarding using dcut & scut values. So what so ever values i keep from 1 to 10 for dcut and 0 to 3 for scut i am getting the same network (even at dcut =1), which i think should not. I am not able to figure out the problem. Please help me .

[Xinqiu Yao]

Hi,

Can you double check your command of using 'cna()'? It should be cm=cm_1_chA, not cm_1_chA=cm_1_chA.

[santosh chaudhary]

Hi, Thank you very much Xin, it was a silly mistake. I want to ask another question about nodal points, some times we know the important residues in the protein and if we mutate it will certainly be inactive. While using this package for calculating node betweenness, it gives a higher value for some residues which are far from the active site and mutating those might not affect its activity, some residues near the active site which are certainly required and for some residues it gives almost zero value of betweeness ( which i know are essential for its activity and mutating it makes protein inactive). why it is so ? How should we interpret the results?

[Barry Grant]

These are questions for you yourself to follow up on. You should think about what betweenness is trying to capture. It is certainly not a sole metric of functional importance - note that functional importance can come from may different contributions. I suggest you visit the literature for guidance beyond the bio3d technical support we provide here.