The DNA strands are there, but they are coming in as individual models. So
we have 60 models (protein + 2 DNA strands) instead of 20 in that assembly
file. It seems to be because the models are not in order. The sequence in
the file goes
protein models 1-20
dna strand models 1-20
dna strand models 1-20
Jmol is not set up to do that. So when it hits a new model, it assigns a
new number. I'm surprised, though, that it is losing the PDB model number
in the file. I will check to see if there is something we can do about
that. It's also possible that we could re-order those.
On Thu, Jan 28, 2016 at 5:33 AM, Angel Herráez <angel.herr...@uah.es> wrote:
> We are starting to work on reading mmCIF files from PDBe, for "assemblies".
> This means the actual biological unit of the molecule, be it monomer,
> dimer,
> tetramer, etc -- manually checked since there are often several
> automatically
> prepared biological units in PDB
>
> Apparently EBI has been applying some variation in which CIF dta fields are
> retained in the assemby CIF file
> So far we have managed (Proteopedia) to handle those idiosyncrasies, but I
> have hit some weird problem with 2LEV
> It has protein + DNA, several models.
> Jmol 14.4.1 Jan 15 fails to render the DNA at all
>
> These are my checks:
>
> load http://www.ebi.ac.uk/pdbe/entry-files/download/pdb2lev.ent
> // PDB file -- ok
>
> load
>
> http://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/structures/divide
> d/pdb/le/pdb2lev.ent.gz
> // PDB file (gz) -- ok
>
> load http://www.ebi.ac.uk/pdbe/entry-files/download/2lev_updated.cif
> // Updated mmCIF file -- ok
>
> load
> http://www.ebi.ac.uk/pdbe/static/entry/download/2lev-assembly-1.cif.gz
> // Assembly 1 (mmCIF; gz) -- DNA is not displayed
> select dna //19040 atoms selected
> hide all //37340 hidden atoms
> display all //0 hidden atoms
> // in all cases, no rendering of DNA
>
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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