Taking an mmtf, converting to pdb, and then back to mmtf yields some funky entity info.
Specifically, take "3zyb", which has 6 entities, the first of is "PA-I galactophilic lectin", with asymIds A through H.
After converting to a pdb and back, we have an unnamed first entity (expected), with asymIds as below.
A,B,C,D,E,F,G,H,C,D,E,F,G,H,D,E,F,G,H,E,F,G,H,F,G,H,G,H,H
I don't think this is desired?
The other entities have the correct number of chains associated (albeit slightly different asymIds, but I think it's a non-issue).
Code to reproduce
MmtfUtils.setUpBioJava();
try {
Structure struc = MmtfActions.readFromFile((new File("/tmp/3zyb.mmtf")).toPath());
System.out.println(struc.getEntityInfos());
Files.write((new File("/tmp/3zyb.pdb")).toPath(), struc.toPDB().getBytes());
Structure struc2 = StructureIO.getStructure((new File("/tmp/3zyb.pdb")).toURI().toURL().toString());
System.out.println(struc2.getEntityInfos());
MmtfActions.writeToFile(struc2, (new File("/tmp/3zyb_weird.mmtf")).toPath());
} catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
Taking an
mmtf, converting topdb, and then back tommtfyields some funky entity info.Specifically, take "3zyb", which has 6 entities, the first of is "PA-I galactophilic lectin", with asymIds A through H.
After converting to a
pdband back, we have an unnamed first entity (expected), with asymIds as below.I don't think this is desired?
The other entities have the correct number of chains associated (albeit slightly different asymIds, but I think it's a non-issue).
Code to reproduce