pdb.annotate error
As per index page: http://thegrantlab.org/bio3d_v2/html/pdb.annotate.html
ids2 <- c("6Q21_B", "1NVW", "1P2U_A")
anno <- pdb.annotate(ids2)throws
Error: Not Found
In addition: Warning message:
In pdb.annotate(ids2) :
ids should be standard 4 character PDB-IDs: trying first 4 characters...sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dyliblocale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8attached base packages:
[1] stats graphics grDevices utils datasets methods baseother attached packages:
[1] bio3d_2.4-1loaded via a namespace (and not attached):
[1] httr_1.4.2 compiler_4.0.3 R6_2.5.0 parallel_4.0.3
[5] tools_4.0.3 RCurl_1.98-1.2 curl_4.3 Rcpp_1.0.5
[9] grid_4.0.3 bitops_1.0-6 XML_3.99-0.5
Comments (4)
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reporter Most likely. Do you recommend a workaround? Thanks in advance for any suggestions
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Should be fixed by this commit
ids2 <- c("6Q21_B", "1NVW", "1P2U_A") anno <- pdb.annotate(ids2) anno[, 1:5] structureId chainId macromoleculeType chainLength experimentalTechnique 6Q21_B 6Q21 B Protein 171 X-ray 1NVW_Q 1NVW Q Protein 166 X-ray 1NVW_R 1NVW R Protein 166 X-ray 1NVW_S 1NVW S Protein 481 X-ray 1P2U_A 1P2U A Protein 166 X-ray
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- changed status to resolved
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possibly related to http://www.rcsb.org/pdb/rest/customReport