pdb.annotate & large structures (.cif only)

Hello,

For a few selected newer pdb entries pdb.annotate throws an error:

Warning in .format_tbl(ret, ids, anno.terms, unique = unique) :
  Annotation data could not be found for PDB ids

This seems to happen for large structure entries where only a PDBx/mmCIF file is available, for example this one:

test <- pdb.annotate("7OAP_A")

Is there a way to fix this? Many thanks in advace!

‌

sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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_2.4-3.9000 RCurl_1.98-1.5 ggrepel_0.9.1 kableExtra_1.3.4 patchwork_1.1.1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[10] readr_2.1.2 tidyr_1.2.0 tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1

loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 svglite_2.1.0 lubridate_1.8.0 ggseqlogo_0.1 assertthat_0.2.1 digest_0.6.29 utf8_1.2.2 R6_2.5.1
[9] cellranger_1.1.0 plyr_1.8.6 backports_1.4.1 reprex_2.0.1 evaluate_0.14 httr_1.4.2 pillar_1.7.0 rlang_1.0.1
[17] curl_4.3.2 readxl_1.3.1 rstudioapi_0.13 rmarkdown_2.11 webshot_0.5.2 bit_4.0.4 munsell_0.5.0 broom_0.7.12
[25] compiler_4.1.2 modelr_0.1.8 xfun_0.29 pkgconfig_2.0.3 systemfonts_1.0.3 htmltools_0.5.2 tidyselect_1.1.1 fansi_1.0.2
[33] viridisLite_0.4.0 crayon_1.4.2 tzdb_0.2.0 dbplyr_2.1.1 withr_2.4.3 bitops_1.0-7 grid_4.1.2 jsonlite_1.7.3
[41] gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2 magrittr_2.0.2 scales_1.1.1 vroom_1.5.7 cli_3.1.1 stringi_1.7.6
[49] fs_1.5.2 xml2_1.3.3 ellipsis_0.3.2 generics_0.1.2 vctrs_0.3.8 tools_4.1.2 bit64_4.0.5 glue_1.6.1
[57] hms_1.1.1 parallel_4.1.2 fastmap_1.1.0 yaml_2.2.2 colorspace_2.0-2 rvest_1.0.2 knitr_1.37 haven_2.4.3

Comments (2)