Web-based alignment for pdb2aln.ind

[Former user]

Hello,

I am following the NMA DHFR part 1 tutorial to project my MD simulation into my PCA space of the crystal structures. My simulation frames are stored on my university's high performance computing cluster and I do not have permission to install the MUSCLE program. I recognize I could transfer these data to my personal computer/external hard drive for analysis, but would rather not due to the size and transfer time. The web.args functionality has been useful for pdbaln and I tried to apply the same idea to pdb2aln.ind, but it does not work:

inds <- pdb2aln.ind(pdbs, pdbref, gaps.res$f.inds, web.args=list(email='[e-mail]'))

I get the error:

Error in (function (aln, id = NULL, profile = NULL, exefile = "muscle", : Sequence-profile alignment is not supported by online web service. Calls: pdb2aln.ind -> pdb2aln -> seq2aln -> do.call -> <Anonymous>

Is it possible modify pdb2aln.ind to include this functionality? Any help with this is greatly appreciated.

[Xinqiu Yao]

Just a quick note: This is something related to an unsupported service (profile-profile alignment) of the EBI server. Currently, the only solution is to install a local MUSCLE or CLUSTAL