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

[Ezra P. <ezr...@rc...>]

1hho does have a non-standard crystal frame. (see remark 285)

If you load the assembly PDB file in rasmol - it displays properly. Pymol
is having the issue.

However, if you fetch the cif file in pymol, and ask it to display the
assembly - it does the right thing.

set assembly, 1
fetch 1hho


Ezra

On Mon, Feb 22, 2016 at 5:04 AM, Spencer Bliven <spe...@gm...>
wrote:

> 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 <ca...@su...>
> 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 <imi...@bi...>
>> 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 <imi...@bi...>
>> > Sent: Monday, February 22, 2016 3:39 AM
>> > To: pym...@li...
>> > 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: imi...@bi...
>> > _________________________________________________
>> > 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: imi...@bi...
>> _________________________________________________
>> Biomedical Research Foundation, Academy of Athens
>> Soranou tou Efessiou 4, 115 27 Athens, Greece
>>
>>
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>
>
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