Find PFAM annotations of PDB entries error

[Dang Wang]

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"
NULL

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?

[Xinqiu Yao]

pdb.pfam is obsolete. Use pdb.annotate() instead.

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[Dang Wang]

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

[Xinqiu Yao]

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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[Xinqiu Yao]

Look into the situation of Pfam and adapt the code to the new service if necessary. https://www.ebi.ac.uk/interpro/

[Dang Wang]

Thank you for your help.