pdb.annotate error

[George Tzotzos]

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 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] bio3d_2.4-1

loaded 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

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[Lars Skjærven]

possibly related to http://www.rcsb.org/pdb/rest/customReport

[George Tzotzos]

Most likely. Do you recommend a workaround? Thanks in advance for any suggestions

[Xinqiu Yao]

Should be fixed by this commit

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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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