pdbs2pdb error

[Former user]

Hi, I'm trying to make the correlation network analysis based in ensemble NMA. When apply the function pdbs2pdb, R gives me the next error

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', obtained 'A'

The code is basically the same that of the vignette

myfiles = c("A", "B", "C") pdbs <- pdbaln(myfiles) refpdb <- pdbs2pdb (pdbs)

Which could be the problem? Thanks in advance

[Lars Skjærven]

Hmm.. hard to say without more information. what is the content of pdbs ? does the argument inds=1 have any effect?

also, check if this code works for you:

files= c(get.pdb("4uxy"), get.pdb("4uxt"))
pdbs = pdbaln(files)
pdbs2pdb(pdbs)

if so, there is probably something wrong with your pdbs object?

[leleonp]

Hi, thanks for your answer. The pdbs object contains pdb files located in my computer. These structures are a set of proteins that were previously modelled and refined with ModRefiner. With this pdbs object, I can do PCA and NMA, however, when I try with pdbs2pdb, I get that error. Thanks in advance. Best regards

[Lars Skjærven]

Could you send me the pdbs object by e-mail ([e-mail])?

save(pdbs, file="mypdbs.RData")

That's the only way I can see to debug this.

[Lars Skjærven]

Bug was related to NA values in the chain component of the pdbs object. This resulted in write.pdb() failing. See bugfix 35f1ce9.

pdbs2pdb() should now work as expected if you update to the development version of bio3d. see frontpage for more info.

Thanks for spotting and reporting this bug.