search

3D-Beacons / 3d-beacons-client

Implementation of the 3D-Beacons client (local 3D model server)
Apache License 2.0
3 stars 6 forks source link

QMEAN API error: "No valid residues could be found in structure" #18

Closed sillitoe closed 2 years ago

sillitoe commented 3 years ago

I want to use the API to remotely generate QMEAN calculations for incoming models.

I submitted one of the PDB structures from the Baker/Pfam models to the web interface and I get the error:

No valid residues could be found in structure

image

PDB file is here: https://github.com/3D-Beacons/3d-beacons-client/raw/master/tests/fixtures/baker_pfam/pdb/PF15324.pdb

I used the pdb_validate tool from pdb-tools to validate the file - this suggested that the looked okay (I'm not sure how rigorous this is):

$ pdb_validate tests/fixtures/baker_pfam/original/pdb/PF15324.pdb 
It *seems* everything is OK.

Note: the PDB file only contains ATOM records.

I tried explicitly adding the following seqres to the web form then resubmitting the PDB file, but I got the same error:

>W5MSL4_LEPOC/119-1387
DIVISQYSVGGKEAVRAVFKERCRSAPVRKAVKVQLLEPQEPPPAGPPPPQPCTADTVAVVTAAAIAATAPLLKAQHDLDTKISSVSELLKKLQHVERQP
CQEERVAELEKQLAALTHQRLQHLEQIQQQQLELQTRLLGGALSAVSGSSAPAPPVSSHLAAPAQPGLQRLPGNASRDESPAGAPASTSTAAAGCPPPRV
PAAETSPLETPAPRRFVPVPMSRDAAARRSQEKPAVEKSKVASGRLGSGRLLEEILNTQGLQSARGRSVTMATGGSYTERNSCSRKAEEAASAAVKKASD
VLRDLGQLKTEMQSLLQEGKEWRSNLEQQSKVPEVFPLEWSRQARPNRGPAASDPPPPPPPPPPAPLEGSLHPLKSASLPQSSDPMVLQKTKAPKSMFED
AEKVLRQVKQHKKVLEENLEAILRANDGAVLHSQIEALSSNRDASGEIRIKKTVDEWIGTISKDIQAEIARKDFVSQMKGKDKEAATVSSQKGQGAKGIR
QQRDVKNAAQSKLITAARKPLNTSKPFRKAAEGHLEKPNVQSKSFSHFLQKKEPILKGQELEDEEYLQRVYGRAVYQGHRSTLKRAPYLRINSPSPKSKP
QRPRVVESVKGIKVKSARTQTGLFPPKKTDSRPAGQPFSHELDYVFSPSRDVPSTGIRSAPLEGLLIPVAIPLGVPRLDGAAPQPSSVTTVQKQPVTVTT
SVPPCPPKPPAGARKPNVALLEMRSEKKDPPTLTVQVLPSVDINSVSSESPAPSPPLAQPNIQTVEQAQTQEEDSNEFPGTDYVAVTDIAQDSEEEDGLS
EAAIEINGQVGPALAPYHGPSFPPSAPEPRPTIDAVEVRIQQRETLENRLVDWVEQQLMARVIAELYPPRVQAAEDSGASELEDSGASTSDIVEAAGGGG
VQLFVEAGVPVDSELIRQYVNDALAETIAIMLGQREGQRPASPPAALEVPAPPKEPVVPTPVPTPQLSPHPSPPPSGRAPSPVRTPDVSERESAAEFSEA
ELEPSAPVHTEPEEEHKSPVITPAATPIPSPHPVATPSPPEPERNPSPEPARPLPSSWEDAQLPLEEEDPRPDREEQQSQRAVVMSVAQEEETVSLVTPS
PPVAPQAPTPTPPPPLQAPPTATETPPPPTPSTEDSSSTASVTETDTAGRNISEGELLFSYGQLAAARALAEGGLTLPNLSASLSSSLHGFQDMDYDPPS
EGQVIRRPDIQHHRDPVLSLLARMNQGLTALQEGHVHPQIHSDDDSSMGEVSEGQRPRLPAAGETLLTG
sillitoe commented 2 years ago

This has been fixed by the good people at SWISSMODEL (thanks Andrew)