unequal vector lengths error in pymol.dccm

[Former user]

Hi all, I have done dccm analysis with the following command line (for selected 60 ns part of 300 ns simulation) for the protein (in dimeric form) with the ligand. It worked fine when have used all residues in but by assigning selected residues by resno = c () (ligand is not included) got the following error for pymol.dccm: Error in pymol.dccm(cij, pdb, exefile = "/usr/bin/pymol-3.6", type = "session") : unequal vector lengths Execution halted Any help will be appreciated. Bests Zahra

dcd <- read.dcd("STING.dcd") pdb <- read.pdb("STING.pdb") inds <- atom.select(pdb, resno = c(1:25,74:99,109:115,185:209,258:283,293:299), elety = "CA") trj <- fit.xyz(fixed = pdb$xyz, mobile = dcd, fixed.inds = inds$xyz, mobile.inds = inds$xyz)

Cross-Correlation Analysis

cij <- dccm(trj[, inds$xyz]) plot(cij) plot.dccm(cij, contour=FALSE, col.regions=bwr.colors(200), at=seq(-1,1,by=0.1) ) pymol.dccm(cij, pdb, exefile="/usr/bin/pymol-3.6",type="session") net <- cna(cij) plot(net, pdb)

[Xinqiu Yao]

Since you trimmed the trajectory (and hence cij), you need to provide a trimmed pdb to pymol.dccm() as well. For example, pymol.dccm(cij, pdb=trim(pdb, inds=inds), …)

[Mahnaz Tehrani]

Dear Xinqiu,

so many thanks. the issue has been fixed!

Cheers

Zahra