ubject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
I thought about this and I think the only workable solution that will keep
everyone happy and maintain the status quo as far as possible is to get an
extra data item added to mmCIF for the parameter combination
multiplicity*oc
I thought about this and I think the only workable solution that will
keep everyone happy and maintain the status quo as far as possible is
to get an extra data item added to mmCIF for the parameter combination
multiplicity*occupancy (I believe this parameter is called the 'site
population' in Shel
On 12/16/10 06:47, Ian Tickle wrote:
>
> For the sake of argument let's say that 0.02 Ang is too big to be
> rounding error. So if you see that big a shift then the intention of
> the refinement program (or rather the programmer) which allowed such a
> value to be appear in the output should be t
> If the difference is insignificant, it may as well be off-axis. I
> guess if the difference is insignificant it just comes down to personal
> preferences.
My point was that if you're being strictly parsimonious with your
parameters then you shouldn't be varying 2 additional parameters if it
p
On 12/16/10 03:06, Ian Tickle wrote:
> Dale
>
>> The reward of the
>> full calculation is that all the complications you describe disappear.
>> An atom that sits 0.001 A from a special position is not unstable
>> in the least.
>
> That's indeed a very interesting observation, I have to admit that
On Thu, Dec 16, 2010 at 1:18 PM, wrote:
> Of course there is no dicontinuity, but you create one the moment you decide
> that certain symmetry operators no longer apply to certain atoms.
Change 'atoms' in that statement to 'reflections', or to 'map grid
points', then read it again. Does the (-
Ooops sorry that's only the executable, I guess to have to contact
David for the source.
-- Ian
On Thu, Dec 16, 2010 at 1:14 PM, Jon Wright wrote:
> On 16/12/2010 12:24, Ian Tickle wrote:
>>>
>>> I think this is how the Oxford CRYSTALS software (
>>> http://www.xtl.ox.ac.uk/crystals.html ), whic
,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle
Sent: Thursday, December 16, 2010 1:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
> You still have an arbitrary thresh
Hi Jon, try this:
http://www.xtl.ox.ac.uk/download.html
-- Ian
On Thu, Dec 16, 2010 at 1:14 PM, Jon Wright wrote:
> On 16/12/2010 12:24, Ian Tickle wrote:
>>>
>>> I think this is how the Oxford CRYSTALS software (
>>> http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at
>>> lea
On 16/12/2010 12:24, Ian Tickle wrote:
I think this is how the Oxford CRYSTALS software (
http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at
least 30 years, deals with this issue, so I can't accept that it can't
be made to work, even if I haven't got all the precise details
str
> You still have an arbitrary threshold: at high resolution you see two
> disordered atoms off-axis and at low resolution you see one ordered atom
> on-axis. However, somewhere in between you or the program has to decide
> whether you still see two atoms or if the data (resolution) does not warr
Ian Tickle
Sent: Wednesday, December 15, 2010 6:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
That's my whole point, it's not an arbitrary threshold, it's determined
completely by what the data are capable of telling you about
Or you could write and ask the author, who is always willing to help (sorry,
David!)...
On 16 Dec 2010, at 11:24, Ian Tickle wrote:
>> I think this is how the Oxford CRYSTALS software (
>> http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at
>> least 30 years, deals with this is
> I think this is how the Oxford CRYSTALS software (
> http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at
> least 30 years, deals with this issue, so I can't accept that it can't
> be made to work, even if I haven't got all the precise details
> straight of how it's done in pract
Dale
> The reward of the
> full calculation is that all the complications you describe disappear.
> An atom that sits 0.001 A from a special position is not unstable
> in the least.
That's indeed a very interesting observation, I have to admit that I
didn't think that would be achievable. But th
cule suddenly becomes
>> > special and the occupancy is set to 1.0. So depending on rounding errors,
>> > different thresholds etc. different programs may make different decisions
>> > on whether a water is special or not.
>> >
>> > For me, this is confusing.
.
>>
>> For me, this is confusing.
>>
>> Best regards,
>> Herman
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian
>> Tickle
>> Sent: Wednesday, December 15, 2010 3:47 PM
>>
ions on whether
> > a water is special or not.
> >
> > For me, this is confusing.
> >
> > Best regards,
> > Herman
> >
> > -Original Message-
> > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian
> > Tickle
&
fferent decisions on whether a water is special or not.
>
> For me, this is confusing.
>
> Best regards,
> Herman
>
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian
> Tickle
> Sent: Wednesday, December 15, 2010 3:47
...@jiscmail.ac.uk] On Behalf Of Ian Tickle
Sent: Wednesday, December 15, 2010 3:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Dear George
I notice that the Oxford CRYSTALS program, which is what I used when I did
small-molecule crystallography
Dear George
I notice that the Oxford CRYSTALS program, which is what I used when I
did small-molecule crystallography and which is still quite popular
among the small-molecule people (maybe not as much as Shel-X!), uses
the CIF convention:
OCC= This parameter defines the site occupancy EXCLUDING
Dear Ian,
Yes. Once an atom has been identified as on a special position because it
is within a specied tolerance, SHELXL applies the appropriate contraints
to both the coordinates and the Uij so there is no danger of the atom
wandering off the special position. Usually, when an atom it very cl
Dear George
I would say that an atom has fractional occupancy (but unit
multiplicity) unless it's exactly on the special position (though I
can foresee problems with rounding of decimal places for an atom say
at x=1/3), so that effectively once the atom is fixed exactly on the
s.p. the symmetry co
Dear Ian,
Of course I could convert the occupancy on reading the atom in and convert
it back agains on reading it out. This is not quite so trivial as it
sounds because I need to set a threshold as to how close the atom has
to be to a special position to be treated as special, and take care
t
Dear George
Is applying the multiplicity factor to the occupancy internally in the
program such a issue anyway? It need only be done once per atom on
input (i.e. you multiply each input occupancy by the multiplicity to
get the combined multiplicity*occupancy value that you would have
reading in d
> Personally I find it disturbing to have the occupancy of "B 31"
> set to 0.33 and that of "D 31" set to 1.00 simply because of an
> insignificant shift in the position of the atom.
>
> Dale Tronrud
H2O on or near a 3-fold must be disordered because obviously H2O only
has 2-fold symmetry. It
BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Hi Gloria,
My hobby is space group symmetry.
My interest phenix development.
so I can't imagine a protein crystallographer would ever need to
apply the modulation function to a protein atom that hap
> > No disorder is involved.
> >
> > The occupancy of an (fully occupied) atom on an n-fold rotation axis is
> 1/n
> > If a two-fold, 1/2
> > If a three-fold, 1/3
> >
> > When you sum over all the atoms in the unit cell, application of the
> symmetry operations to atoms lying on the rotation axis g
SHELXL also expects that the occupancy of a fully occupied atom on a
threefold axis should be set at 1/3, and will generate this automatically
if necessary. It will also generate automatically the necessary
constraints for the x, y and z parameters (and for the Uij if the atom is
anisotropic). I
ckle
Date: Saturday, December 11, 2010 0:41
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
To: CCP4BB@JISCMAIL.AC.UK
> No that surely can't be right. Application of a symmetry
> operator to
> a point on a special position which is unchanged by the operator
> do
On Fri, 2010-12-10 at 22:40 +, Ian Tickle wrote:
> Application of a symmetry operator to
> a point on a special position which is unchanged by the operator
> doesn't generate a symmetry copy of the point, because there is no
> symmetry copy of such a point!
Why not? Symmetry-related copy may
On Fri, 2010-12-10 at 21:53 +, Ian Tickle wrote:
> Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the
> special position
Shouldn't 1/3 be better for programming purposes? If you set occupancy
to 1.0, then you should specify that symmetry operators do not apply for
these atom
No that surely can't be right. Application of a symmetry operator to
a point on a special position which is unchanged by the operator
doesn't generate a symmetry copy of the point, because there is no
symmetry copy of such a point! For general Wyckoff positions it does,
for sure. If you look at
The proper occupancy for an atom on a special position depends on
how one defines the meaning of the number in that column. In the
past, refinement programs, at least I know mine did, simply expanded
all atoms in the coordinate file by the symmetry operators to determine
the contents of the uni
Good point Colin! 2-Zn insulin is of course a classic example of
this, where the two independent Zn2+ ions both sit on the
crystallographic 3-fold in R3. It doesn't matter whether you count
the metal ion as part of the protein or not: if I understand Gloria's
original question correctly, all that
Colin Nave wrote:
..
Also Acta Cryst. (2002). D58, 29-38 "The 2.6 Å resolution structure of Rhodobacter
capsulatus bacterioferritin with metal-free dinuclear site and heme iron in a
crystallographic `special position' "D. Cobessi, L.-S. Huang, M. Ban, N. G. Pon, F.
Daldal and E. A. Berry ( h
Does one regard the metal atom in a metalloprotein as being part of the protein?
If so, a shared metal could occupy a special position in a dimer for example.
In Acta Cryst. (2008). D64, 257-263 "Metals in proteins: correlation between
the metal-ion type, coordination number and the amino-acid
: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
The forces acting on an atom at a special position must have the same symmetry
on average as the special position, so the atom will be in equilibrium, and
there will at first sight be no net force (i.e. zero energy gradient) to push
positions.
>
> Best,
> Herman
>
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Ian Tickle
> Sent: Thursday, December 09, 2010 3:35 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and
> How many of you have ever had a protein atom on a Wyckoff position
> (AKA a special position).
Sorry one final comment! On a point of terminology: a Wyckoff
position is _not_ another name for a special position, it's a
descriptor of a set of positions in the unit cell of a space group
which sha
onal cases will occupy "true" Wyckoff
positions.
Best,
Herman
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Ian Tickle
Sent: Thursday, December 09, 2010 3:35 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positio
> cases out there (and so far I have heard of a disulfide bond on a
> 2-fold connecting two homodimers).
I'm slightly puzzled by this example. If the S-S bond is on the
special position, then the rest of the molecule can't have 2-fold
symmetry, so would have to be rotationally disordered with occ
y axes.
>
> Best,
> Herman
>
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Ralf W. Grosse-Kunstleve
> Sent: Thursday, December 09, 2010 3:47 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff pos
] On Behalf Of
Ralf W. Grosse-Kunstleve
Sent: Thursday, December 09, 2010 3:47 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
Hi Gloria,
My hobby is space group symmetry.
My interest phenix development.
> so I can't imagine a protein crys
that it isn't important to handle them in a special way. So Wyckoff
positions remain foreign in the macromolecular context.
Ralf
- Original Message
> From: Gloria Borgstahl
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Wed, December 8, 2010 12:16:54 PM
> Subject: [ccp4bb] Fw
I've gotten some interesting responses, that I will summarize for the
group later, but I thought I should clarify why I asked.
I was worrying about this because I have been working out the steps in
how to determine the (3+1)D superspace group for a protein crystal.
The last step listed in IT vol C
My fellow crystallographers,
I wanted to take a poll.
How many of you have ever had a protein atom on a Wyckoff position
(AKA a special position).
What kind of molecules have you found at special positions (it would
have to contain the symmetry of the special position, right?)
I'm thinking it is i
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