Find PFAM annotations of PDB entries error
Issue #910
new
pdb.pfam(c("6Q21_A", "1NVW", "1P2U_A"))
Unknown IO errorfailed to load external entity "http://www.rcsb.org/pdb/rest/hmmer?structureId=6Q21,1NVW,1P2U"
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I am trying to find PFAM annotations of PDB entries, but I get the following error. I suspect that the PFAM URL has changed. Could you guide me, please?
Comments (5)
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reporter Dear Xinqiu,
Thanks for your reply, I also get the new error when running another code about “pfam”, how do I fix it, please?
Thanks again for your help.
#get sequence of Ecoli DHFR seq <- get.seq("1rx2_A") #scan the Pfam database for our sequence pfam <- hmmer(seq, type="hmmscan", db="pfam") pfam$hit.tbl #download pfam alignment for the DHFR family pfam.aln <- pfam(pfam$hit.tbl$acc[1]) https://pfam-legacy.xfam.org/</a> </code> </div> </section> </main> </body></html>/alignment/seed/format?format=fasta Error in pfam(pfam$hit.tbl$acc[1]) : Url does not exist
Bests,
Dang
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It seems that Pfam is shut down. https://www.ebi.ac.uk/interpro/
We will look into it. For now, I am not sure if it is temporary or permanent.
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- changed version to v2.4/3.0 [future]
- changed component to ToDo
Look into the situation of Pfam and adapt the code to the new service if necessary. https://www.ebi.ac.uk/interpro/
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reporter Thank you for your help.
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pdb.pfam is obsolete. Use pdb.annotate() instead.