Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]

[Robert H. <ha...@st...>]

Ioannis,

I suggest using the CIF file from EBI instead:

http://www.ebi.ac.uk/pdbe/static/entry/download/1hho-assembly-1.cif.gz

It looks good to me -- just one model.

For reference, the RCSB site is using Jmol and is simply loading 1HHO
itself and constructing the assembly *in situ *using the symmetry operators
in that file, not reading the assembly file.  PyMOL must have a simple way
to do that as well. Right? Or do you have to load the assembly file?

There is no mistake in the PDB assembly file. Jmol also reads that just
fine, but as you point out, it is in the form of two models, for reasons I
do not understand. It looks to me like when the PDB assembly file is
created, each BIOMT transformation is put into a separate model. This is
NOT what EBI does when they create the analogous mmCIF assembly file.

A totally different multi-model (NMR solution) issue has been noticed with
CIF assembly files from EBI. [e.g.
http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz] In
that case, there are 20 models, and the atom ordering ens up by chain, not
be model, so that the coordinates for each "model" are scattered
throughout  the file, which seems quite odd to me. And I notice that RCSB
also creates a PDB assembly file for 2lev, but in that case only one model
is produced, and it is just the first NMR model. So this is still an
imperfect design all around. In both cases, I my opinion, there are design
flaws. Don't know that you can call that a bug....

Bob Hanson