Issue loading multi model PDB file

[giagitom]

Hi, This multi model file nucleicModel.pdb.txt presents broken atomic connections in state 2, 3 and 5. I have found the issue is due to the position of the first ENDMDL record. Moving it immediately after CONNECT records restores the correct atomic connections.

[speleo3]

The problem is that the models are not homogeneous. ATOM 1 from the first model is different from ATOM 1 in the second model, and bonds are specified by atom ID. According to the PDB spec, all models should be homogeneous.

It seems there is currently no sane way to load this into PyMOL. I've tried different connect_mode options and discrete loading. Whether the PDB parser can be modified to support such data without breaking something else needs some careful investigation.

[giagitom]

Hi Thomas, I understand.. This is certainly a non standard pdb file format

[speleo3]

The easiest way to load this is to replace MODEL by HEADER (search and replace using your favorite text editor), then PyMOL will load 5 independent objects.