pdbaln throws an error with specific PDB, cif or xml files

[Matthew Watson]

I have been trying to use ICA and PCA on a small set (three members) of large (Ribosomal) complexes.

I first tried to load the files from PDBs but obtained the following error

Warning messages:
1: In read.pdb(files[i]) : duplicated element numbers ('eleno') detected
2: In read.pdb(files[i]) : duplicated element numbers ('eleno') detected
3: In read.pdb(files[i], verbose = FALSE, ...) :
duplicated element numbers ('eleno') detected
4: In read.pdb(files[i], verbose = FALSE, ...) :
duplicated element numbers ('eleno') detected

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I established that one of the files could be loaded individually as a PDB while the other two returned the same error.

I read that a similar issue had been due to the mixture of upper and lowercase chain IDs in files but that using cif or xml files could get around this issue.

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Hence, I tried to load the files as cifs, but this returned the following error

Error in .read_pdb(file, multi = multi, hex = hex, maxlines = maxlines, :
Could not convert string to double (" ? -52.0")

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I tried from xml files but obtained the error

Error in matrix(if (is.null(value)) logical() else value, nrow = nr, dimnames = list(rn, :
length of 'dimnames' [2] not equal to array extent

I have attached the cif files

What should I do?

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[Xinqiu Yao]

Hi,

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I can read all the three files. What version of bio3d do you use? (Type sessionInfo() to check). Maybe you need to update to the latest version, 2.4-1.

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[Matthew Watson]

I updated to the latest version, although the files will are read the same error is returned as before when trying to use pdbaln and subsequently perform ICA

[Xinqiu Yao]

Try to build a pdb list object and then call pdbaln(). For example,

pdblist <- lapply(c("5nco", "5gae", "4v6m"), read.cif)
pdbs <- pdbaln(pdblist)

Please check carefully if the alignment and other attributes look okay. I didn’t test extensively.

[Matthew Watson]

It gets as far as finding the ICA now OK, but returns the following error at this step

xyz <- pdbfit( pdbs, core.inds, outpath = "C:/Users/fbsmawadmin/Desktop/ongoing work/RNC_insertion/PyMOL/YEG_RIBO")
Note: Accessing on-line PDB file
Error in read.pdb(full.files[i], ...) : Error in reading PDB file 1
In addition: Warning messages:
1: In download.file(get.files[k], put.files[k], quiet = !verbose) :
cannot open URL 'https://files.rcsb.org/download/seq1.pdb': HTTP status was '404 Not Found'
2: In file.remove(put.files[k]) :
cannot remove file 'C:\Users\FBSMAW~1\AppData\Local\Temp\Rtmpslkw2Q/seq1.pdb', reason 'No such file or directory'
3: In get.pdb(file, path = tempdir(), verbose = FALSE) :
Some files could not be downloaded, check returned value

However, trying
pca(pdbs, core.find=TRUE, fit=FALSE)

did generate something without throwing an error but the parts of the complex in which I was particularly interested had been omitted.

[Matthew Watson]

I’m having a somewhat similar issue with pdbaln on a list of locally saved PDB files
myfiles <- list.files(path="C:/Users/fbsmawadmin/Desktop/ongoing work/RNC_insertion/PyMOL/all_domain_Sec/various/translocons_only/New folder", pattern=".pdb", full.names=TRUE)

pdbs<- pdbaln(myfiles, fit=TRUE)

Reading PDB files:
C:/Users/fbsmawadmin/Desktop/ongoing work/RNC_insertion/PyMOL/all_domain_Sec/various/translocons_only/New folder/pro_2zjs.pdb
C:/Users/fbsmawadmin/Desktop/ongoing work/RNC_insertion/PyMOL/all_domain_Sec/various/translocons_only/New folder/pro_2zqp.pdb
C:/Users/fbsmawadmin/Desktop/ongoing work/RNC_insertion/PyMOL/all_domain_Sec/various/translocons_only/New folder/pro_3bo0.pdb
C:/Users/fbsmawadmin/Desktop/ongoing work/RNC_insertion/PyMOL/all_domain_Sec/various/translocons_only/New folder/pro_3bo1.pdb
C:/Users/fbsmawadmin/Desktop/ongoing work/RNC_insertion/PyMOL/all_domain_Sec/various/translocons_only/New folder/pro_3din.pdb
.....

Extracting sequences
MUSCLE v3.8.31 by Robert C. Edgar

Error in read.fasta.pdb(s, prefix = "", pdbext = "", pdblist = files, :
No corresponding PDB files found

Any ideas?