I was having trouble waking up that day. Missing residues are common that leave gaps in the resSeq field. I think I was trying to reconcile this with what I was seeing using Bio3d to constructs a contact maps. It automatically renumbers. It is easy enough to go back and recover the resSeq fields from the contact map indices.
resno fields within a pdb file
Are the resno fields within the ATOM records of PDB files within a single chain always consecutive? I understand insertion codes may be present. Aside from that, are they always consecutive regardless of what index they start at?
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I do not know of such a rule in pdb file format specification ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf . Information about some atoms or residues can be missing and if so there is a section in remarks describing what exactly is missing with some comments like why it is missing and so on. I do not remember very well.
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