This looks like a bug in the PDB's file, and you should definitely let them
know about it. It's a particularly weird case since the second model
doesn't correspond to any of the valid crystallographic operators. Probably
it is a problem with the very non-standard crystal frame specified by the
SCALE matrix in the PDB file. These are always problematic, to the point
that some tools (e.g. EPPIC <http://eppic-web.org>) will ignore them
completely.
While waiting for the PDB to fix the file, you can generate the biological
unit from the symmetry operators using:
fetch 1hho, async=0
symexp sym, 1hho, 1hho, 2
-Spencer
On Mon, Feb 22, 2016 at 10:19 AM, Jame R.Ketudat-Cairns <cai...@sut.ac.th>
wrote:
> Dear Ioannis,
> I was wondering about that, too. Given the prominence of hemoglobin
> structure and oxygen binding in Biochemistry education, the 1 HHO structure
> seems to be a bad biological structure to calculate incorrectly. I guess
> an email to the PDB might be in order (if it is intentional, they could at
> least explain it in that case).
> Best Regards,
> Jim
> ________________________________________
> From: Ioannis Michalopoulos <imicha...@bioacademy.gr>
> Sent: Monday, February 22, 2016 4:05 PM
> To: Jame R.Ketudat-Cairns
> Subject: Re: [PyMOL] PyMOL split_states error on [PDB: 1hho]
>
> Dear Jim,
>
> Thank you for your prompt answer which worked perfectly. I was writing a
> tutorial for my students and I found many incorrectly calculated biological
> units. I wonder if we should complain to PDB about it, or wait and see what
> PyMOL can do about it, first.
>
> Best Regards,
>
> Ioannis
>
> On Monday 22 of February 2016 02:09:05 you wrote:
> > Dear Ioannis,
> > The 1HHO biological unit seems to be calculated incorrectly (just spun
> > around the y-axis 180 degrees). I found that the symexp command works
> for
> > this: symexp sym, 1hho, (1hho), 1
> > Best Regards,
> > Jim
> > ________________________________________
> > From: Ioannis Michalopoulos <imicha...@bioacademy.gr>
> > Sent: Monday, February 22, 2016 3:39 AM
> > To: pymol-users@lists.sourceforge.net
> > Subject: [PyMOL] PyMOL split_states error on [PDB: 1hho]
> >
> > Dear PyMOL users,
> >
> > I run PyMOL 1.8.0.0 for Windows.
> >
> > I loaded the biological assembly of 1HHO:
> >
> > http://www.rcsb.org/pdb/files/1HHO.pdb1.gz
> >
> > When I tried:
> >
> > split_states 1hho
> >
> > PyMOL failed to produce the proper tetramer that is seen at:
> >
> >
> http://www.rcsb.org/pdb/explore/jmol.do?structureId=1HHO&opt=3&bionumber=1
> >
> > Instead PyMOL shows a weird tetramer. Is it a bug? This approach works
> > fine on other cases eg 1SVC. Is there any other way to do it?
> >
> > Thank you in advance.
> >
> > Best Regards,
> >
> > Ioannis
> > --
> > Dr Ioannis Michalopoulos
> > Staff Research Scientist - Associate Professor Level
> > Centre of Systems Biology
> >
> > Tel: +30 210 6597 127
> > Fax: +30 210 6597 545
> > Email: imicha...@bioacademy.gr
> > _________________________________________________
> > Biomedical Research Foundation, Academy of Athens
> > Soranou tou Efessiou 4, 115 27 Athens, Greece
> >
> >
> >
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> --
> Dr Ioannis Michalopoulos
> Staff Research Scientist - Associate Professor Level
> Centre of Systems Biology
>
> Tel: +30 210 6597 127
> Fax: +30 210 6597 545
> Email: imicha...@bioacademy.gr
> _________________________________________________
> Biomedical Research Foundation, Academy of Athens
> Soranou tou Efessiou 4, 115 27 Athens, Greece
>
>
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