Error: XML content does not seem to be XML

[Mehdijoodaki]

Hi! I use package ‘bio3d’ version 2.3-3 to calculate protein structure similarity, but when i use "pdbaln" command face with the flowing error! I run modified seqaln.R in R console but again i face with this error. I do not now how update package bio3d! Please help me! thank you!

my Error: "Error: XML content does not seem to be XML: '{"types":[{"identifier":"out","label":"Tool Output","description":"The output from the tool itself","mediaType":"text/plain","fileSuffix":"txt"},{"identifier":"sequence","label":"Input Sequences","description":"Your input sequences as seen by the tool","mediaType":"text/plain","fileSuffix":"txt"},{"identifier":"aln-fasta","label":"Alignment in FASTA format","description":"The alignment in FASTA format","mediaType":"text/plain","fileSuffix":"fasta"},{"identifier":"phylotree","label":"Phylogenetic Tree","description":"The phylogenetic tree","mediaType":"text/plain","fileSuffix":"ph"},{"identifier":"pim","label":"Percent Identity Matrix","description":"The percent identity matrix output file","mediaType":"text/plain","fileSuffix":"pim"}]}' In addition: Warning message: running command 'muscle -version' had status 127 "

[Xinqiu Yao]

Hi,

Please install the developmental version (which contains the bug fixes) following this instruction: https://bitbucket.org/Grantlab/bio3d/wiki/How%20to%20download%20and%20install%20the%20development%20version

Let me know if you have further questions.

[Mehdijoodaki]

Hi! I used " install_bitbucket("Grantlab/bio3d", subdir="ver_devel/bio3d/") to install the development version bio3d package, but again i face with other error " Installation failed: Failed to connect to bitbucket.org port 443: Timed out" !! I used other ways(Git & manual) to install development version , but again exist error!

I really Confused! I don know what to do!

Thank you for your handling!

[Xinqiu Yao]

Since you can't run install_bitbucket(), I guess it might be the problem of Internet connection. I recommend download and install local alignment programs (muscle or clustalo). For example, you can download muscle here: https://www.drive5.com/muscle/downloads.htm

[Mehdijoodaki]

Hello yes!! my problems was from internet connection.
I success to correct my connection. but when i install the development version bio3d package, the following error "my Error: "Error: XML content does not seem to be XML" still exists.

[Xinqiu Yao]

Could you provide the full commands you used and, if possible, examples (such as PDB IDs) to let us reproduce the errors?

[Mehdijoodaki]

library(bio3d)

ids <- c("1TND_B","1AGR_A","1FQJ_A","1TAG_A","1GG2_A","1KJY_A")

raw.files <- get.pdb(ids)

files <- pdbsplit(raw.files, ids)

pdbs <- pdbaln(files)

I think, in the last command, you must add a fake email!

[Xinqiu Yao]

Will test and and see if it runs without a local muscle. But I strongly recommend install MUSCLE on your local machine, and then you won't need to access online server for sequence alignment anymore.

[Mehdijoodaki]

yes i install MUSCLE on my windows, when i run it, noting just happend.

[Mehdijoodaki]

is there a tutorial for use MUSCLE? I do not know how use it!

[Xinqiu Yao]

Bio3d recognizes some locations on Windows but not all. The simplest way is to put muscle under C:\Program Files\ and name it “muscle.exe”

Alternatively, provide the full path to muscle in calling ‘pdbaln’ or ‘seqaln’, using the ‘exefile’ argument.

[Mehdijoodaki]

Tank you i try to solve this problem.

[Xinqiu Yao]

Specific to user's local env, not a bug.

[Mehdijoodaki]

Hi I have new problem! when i run "rmsd " for calculate structure similarity proteins there is below error ! my code " rmsd( pdbs,fit = TRUE ) "

Error: Error in fit.xyz(fixed = x, mobile = y, fixed.inds = 1:length(x)) : length of 'fixed.inds' != length of 'mobile.inds'

please help me!

Thank you!

[Xinqiu Yao]

See issue #557 for the new question. The original question in this issue has been answered.