Re: [COOT] absolute map levels

2022-05-02 Thread Phil Jeffrey
Later in refinement the missing water molecule will also have a higher 
peak because the phases will be better (e.g. your R-free is 20% lower). 
 The fact that it was placed later in refinement both reflects the RMSD 
effect but also reflects the fact that it's more obviously a legitimate 
water late in refinement.


This isn't a phenomenon restricted to macromolecular refinements.

The peak heights are not the same during refinement, and I scroll around 
the levels all the time to look for things that I might have missed, 
including in one case an entire monomer that *was* lurking in the noise 
level in the map since it was being clobbered by solvent flattening.  It 
was also partial occupancy.


While e/Å^3 is probably a better measure than RMSD, it's not a panacea 
and there is no universal ideal contour level - it must be chosen on its 
merits every single time.  The contour level you want to use while 
looking at the partially-occupied monomer is unquestionably lower than 
the one you'd use while looking at the best-ordered monomer in the map - 
and there's always better and worse parts of the asymmetric unit and 
better and worse parts of any monomer.  Changing the units has no effect 
on that.


Phil Jeffrey
Princeton



On 5/2/22 3:19 PM, Dale Tronrud wrote:
    If you view the value of the density as the number of electrons per 
cubic Angstrom relative to the local average it is both accurate and 
precise.  This framing avoids the most serious problems with a measure 
based on the rms, such as the problem that the "rms" depends on the 
particular volume of space calculated (how much of the bulk solvent 
region is included) and what stage of refinement is the project (late in 
refinement the difference map will have a much smaller rmsd and the same 
missing water molecule will have a much taller peak.).


    When a map is viewed at a particular contour based on e/A^3 a 
missing atom will tend to have the same difference map peak height in 
all stages, while the height will vary all over the place when the 
contour is based rmsd.  When I watch people model building I see many 
scrolling the contour level up and down without regard for the numeric 
value of the level, apparently just choosing a value that makes the 
peaks appear the way they prefer the peaks to appear.  This way of 
choosing a contour level seems dangerous to me as it seems to bias the 
appearance of the map towards the modeler's expectation.


Dale Tronrud

On 5/2/2022 11:51 AM, Tim Gruene wrote:

Hi Ian,

thanks - this makes it clear(er) to me. The unit [e/A^3] suggested an
accuracy to me that isn't really there, while rmsd felt more what it
really is (maybe only due to habit and training).

Cheers,
Tim

On Mon, 2 May 2022 15:27:13 +0100
Ian Tickle  wrote:


Hi Tim

I would say that it's not the displayed map density value in whatever
units that's arbitrary: it's completely defined as the true density
on an absolute scale minus the F000 contribution ('b' below) and
optionally divided by the RMS.  It's just that we don't have a good
estimate of F000 and as I said it's your choice of contour level
that's arbitrary.

The Buster map is scaled to the model so is on an absolute scale.  We
can write the linear transformation:

rho[map] = a.(rho[true] - b)

where the scale factor a = 1 so that rho[map] is on the same absolute
scale as rho[true] (i.e. differences in rho[true] are equal to
differences in rho[map]), and b is the F000 contribution.

Cheers

-- Ian


On Mon, 2 May 2022 at 15:04, Tim Gruene 
wrote:


Hi Paul,

I'd rather you comment on the unit "e/A^3" displayed at the top of
my Coot canvas when I change the contour level of a map. Is this
arbitrary?

I noticed that the Buster Wiki states that their FWT is on an
absolute scale. Would there be a paper or url to advance my rusty
habits?

Cheers,
Tim


On Mon, 2 May 2022 13:52:05 +0100 Paul Emsley
 wrote:

On 02/05/2022 12:44, John R Helliwell wrote:

I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather
than 3.



It's 5.6 now :-)

 



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Re: [COOT] absolute map levels

2022-05-02 Thread Dale Tronrud
   If you view the value of the density as the number of electrons per 
cubic Angstrom relative to the local average it is both accurate and 
precise.  This framing avoids the most serious problems with a measure 
based on the rms, such as the problem that the "rms" depends on the 
particular volume of space calculated (how much of the bulk solvent 
region is included) and what stage of refinement is the project (late in 
refinement the difference map will have a much smaller rmsd and the same 
missing water molecule will have a much taller peak.).


   When a map is viewed at a particular contour based on e/A^3 a 
missing atom will tend to have the same difference map peak height in 
all stages, while the height will vary all over the place when the 
contour is based rmsd.  When I watch people model building I see many 
scrolling the contour level up and down without regard for the numeric 
value of the level, apparently just choosing a value that makes the 
peaks appear the way they prefer the peaks to appear.  This way of 
choosing a contour level seems dangerous to me as it seems to bias the 
appearance of the map towards the modeler's expectation.


Dale Tronrud

On 5/2/2022 11:51 AM, Tim Gruene wrote:

Hi Ian,

thanks - this makes it clear(er) to me. The unit [e/A^3] suggested an
accuracy to me that isn't really there, while rmsd felt more what it
really is (maybe only due to habit and training).

Cheers,
Tim

On Mon, 2 May 2022 15:27:13 +0100
Ian Tickle  wrote:


Hi Tim

I would say that it's not the displayed map density value in whatever
units that's arbitrary: it's completely defined as the true density
on an absolute scale minus the F000 contribution ('b' below) and
optionally divided by the RMS.  It's just that we don't have a good
estimate of F000 and as I said it's your choice of contour level
that's arbitrary.

The Buster map is scaled to the model so is on an absolute scale.  We
can write the linear transformation:

rho[map] = a.(rho[true] - b)

where the scale factor a = 1 so that rho[map] is on the same absolute
scale as rho[true] (i.e. differences in rho[true] are equal to
differences in rho[map]), and b is the F000 contribution.

Cheers

-- Ian


On Mon, 2 May 2022 at 15:04, Tim Gruene 
wrote:


Hi Paul,

I'd rather you comment on the unit "e/A^3" displayed at the top of
my Coot canvas when I change the contour level of a map. Is this
arbitrary?

I noticed that the Buster Wiki states that their FWT is on an
absolute scale. Would there be a paper or url to advance my rusty
habits?

Cheers,
Tim


On Mon, 2 May 2022 13:52:05 +0100 Paul Emsley
 wrote:
  

On 02/05/2022 12:44, John R Helliwell wrote:

I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather
than 3.



It's 5.6 now :-)



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--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [COOT] absolute map levels

2022-05-02 Thread Tim Gruene
Hi Ian,

thanks - this makes it clear(er) to me. The unit [e/A^3] suggested an
accuracy to me that isn't really there, while rmsd felt more what it
really is (maybe only due to habit and training).

Cheers,
Tim

On Mon, 2 May 2022 15:27:13 +0100
Ian Tickle  wrote:

> Hi Tim
> 
> I would say that it's not the displayed map density value in whatever
> units that's arbitrary: it's completely defined as the true density
> on an absolute scale minus the F000 contribution ('b' below) and
> optionally divided by the RMS.  It's just that we don't have a good
> estimate of F000 and as I said it's your choice of contour level
> that's arbitrary.
> 
> The Buster map is scaled to the model so is on an absolute scale.  We
> can write the linear transformation:
> 
> rho[map] = a.(rho[true] - b)
> 
> where the scale factor a = 1 so that rho[map] is on the same absolute
> scale as rho[true] (i.e. differences in rho[true] are equal to
> differences in rho[map]), and b is the F000 contribution.
> 
> Cheers
> 
> -- Ian
> 
> 
> On Mon, 2 May 2022 at 15:04, Tim Gruene 
> wrote:
> 
> > Hi Paul,
> >
> > I'd rather you comment on the unit "e/A^3" displayed at the top of
> > my Coot canvas when I change the contour level of a map. Is this
> > arbitrary?
> >
> > I noticed that the Buster Wiki states that their FWT is on an
> > absolute scale. Would there be a paper or url to advance my rusty
> > habits?
> >
> > Cheers,
> > Tim
> >
> >
> > On Mon, 2 May 2022 13:52:05 +0100 Paul Emsley
> >  wrote:
> >  
> > > On 02/05/2022 12:44, John R Helliwell wrote:  
> > > > I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather
> > > > than 3.  
> > >
> > >
> > > It's 5.6 now :-)
> > >
> > > 
> > >
> > > To unsubscribe from the COOT list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
> > >
> > > This message was issued to members of www.jiscmail.ac.uk/COOT, a
> > > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> > > available at https://www.jiscmail.ac.uk/policyandsecurity/  
> >
> >
> >
> > --
> > --
> > Tim Gruene
> > Head of the Centre for X-ray Structure Analysis
> > Faculty of Chemistry
> > University of Vienna
> >
> > Phone: +43-1-4277-70202
> >
> > GPG Key ID = A46BEE1A
> >
> > 
> >
> > To unsubscribe from the COOT list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/COOT, a
> > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> > available at https://www.jiscmail.ac.uk/policyandsecurity/
> >  



-- 
--
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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [COOT] absolute map levels

2022-05-02 Thread Ian Tickle
Hi Tim

I would say that it's not the displayed map density value in whatever units
that's arbitrary: it's completely defined as the true density on an
absolute scale minus the F000 contribution ('b' below) and optionally
divided by the RMS.  It's just that we don't have a good estimate of F000
and as I said it's your choice of contour level that's arbitrary.

The Buster map is scaled to the model so is on an absolute scale.  We can
write the linear transformation:

rho[map] = a.(rho[true] - b)

where the scale factor a = 1 so that rho[map] is on the same absolute scale
as rho[true] (i.e. differences in rho[true] are equal to differences in
rho[map]), and b is the F000 contribution.

Cheers

-- Ian


On Mon, 2 May 2022 at 15:04, Tim Gruene  wrote:

> Hi Paul,
>
> I'd rather you comment on the unit "e/A^3" displayed at the top of my
> Coot canvas when I change the contour level of a map. Is this arbitrary?
>
> I noticed that the Buster Wiki states that their FWT is on an absolute
> scale. Would there be a paper or url to advance my rusty habits?
>
> Cheers,
> Tim
>
>
> On Mon, 2 May 2022 13:52:05 +0100 Paul Emsley
>  wrote:
>
> > On 02/05/2022 12:44, John R Helliwell wrote:
> > > I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather than
> > > 3.
> >
> >
> > It's 5.6 now :-)
> >
> > 
> >
> > To unsubscribe from the COOT list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/COOT, a
> > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> > available at https://www.jiscmail.ac.uk/policyandsecurity/
>
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
>
> This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing
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Re: [COOT] absolute map levels

2022-05-02 Thread Tim Gruene
Hi Paul,

I'd rather you comment on the unit "e/A^3" displayed at the top of my
Coot canvas when I change the contour level of a map. Is this arbitrary?

I noticed that the Buster Wiki states that their FWT is on an absolute
scale. Would there be a paper or url to advance my rusty habits?

Cheers,
Tim


On Mon, 2 May 2022 13:52:05 +0100 Paul Emsley
 wrote:

> On 02/05/2022 12:44, John R Helliwell wrote:
> > I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather than
> > 3.  
> 
> 
> It's 5.6 now :-)
> 
> 
> 
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
> 
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> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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-- 
--
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Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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Re: [COOT] absolute map levels

2022-05-02 Thread Paul Emsley

On 02/05/2022 12:44, John R Helliwell wrote:

I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather than 3.



It's 5.6 now :-)



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Re: [COOT] absolute map levels

2022-05-02 Thread John R Helliwell
Dear Tim,
I recall initiating a similar thread, and question, some years back. 
Ian may have answered similarly before. 
I was intrigued by Paul’s 5sigma Fo-Fc default cut off, rather than 3. But in 
practice as i delved in peaks below 5sigma I generally found, and still find, 
in many cases what are just obviously noise. Also I think it is good to have a 
consistent convention within Coot, listing as a default those peaks above 
5sigma, if only as a place to start. 
[This unfortunately doesn’t answer your question.]
Greetings,
John 

Emeritus Professor John R Helliwell DSc




> On 2 May 2022, at 07:45, Tim Gruene  wrote:
> 
> Hello readers,
> 
> how does Coot calculate the absolute map levels, i.e. the contour level
> given as [e/A^3]? i always thought (rather from hear-say) that F000 was
> necessary for the absolute level. With a small molecule structure, F000
> can be calculated from a complete model, but with solvent channels, the
> number of disordered electron is not known, is it?
> 
> Thanks a lot for a clarification!
> 
> Best,
> Tim
> 
> 
> -- 
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
> 
> Phone: +43-1-4277-70202
> 
> GPG Key ID = A46BEE1A
> 
> 
> 
> To unsubscribe from the COOT list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
> 
> This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list 
> hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [COOT] absolute map levels

2022-05-02 Thread Ian Tickle
Hi Tim

The absolute peak height doesn't only depend on the element, it also
depends on a number of other things, most notably the resolution and the B
factor (i.e. peaks are broader and peak heights are lower at lower
resolution and higher B factor), and of course the occupancy factor in the
case of partial occupancy.  So I'm not clear how one would know what peak
height to expect just by looking at the map: one would have to do quite a
complicated calculation involving a Fourier transform of the scattering
curve.  It's the volume integral of the electron density under the peak
that's directly related to the element type, not the peak height.  The
range of resolution and B factor for small molecules is much less than for
macromolecules, so your method of element identification is likely to be
much more reliable in the former case.

Cheers

-- Ian


On Mon, 2 May 2022 at 12:15, Tim Gruene  wrote:

> Hi Ian,
>
> this is the custom I was educated with. However, small molecule people
> seem confused when a map contour level is described with an rsmd (which
> to me makes some sense). When refining a structure with shelxl, the
> peak height of the maxima of the difference map corresponds quite well
> to the element one is expecting, i.e. the absolute value of the peak
> height can be used to guess the missing atom type (e.g. '8' for a
> properly ordered oxygen from a water molecule).
>
> Also COOT has been displaying the map countour level with the unit
> e/A^3, and I seem to remember Paul's recommendation to use this unit,
> rather than the rmsd, which is displayed in brackets.
>
> Cheers,
> Tim
>
> On Mon, 2 May 2022 09:48:30 +0100 Ian Tickle  wrote:
>
> > Hi Tim
> >
> > F000 is customarily not included in MX electron density for the
> > reason you mention.  This doesn't matter because the contour levels
> > are completely arbitrary anyway, i.e. you choose a level that shows
> > the features you expect to see.  This can be misleading of course
> > since there may be significant features at lower density than you
> > expected due to thermal motion / disorder or maybe H atoms; however
> > including F000 would not change that.
> >
> > Cheers
> >
> > -- Ian
> >
> >
> > On Mon, 2 May 2022 at 07:45, Tim Gruene 
> > wrote:
> >
> > > Hello readers,
> > >
> > > how does Coot calculate the absolute map levels, i.e. the contour
> > > level given as [e/A^3]? i always thought (rather from hear-say)
> > > that F000 was necessary for the absolute level. With a small
> > > molecule structure, F000 can be calculated from a complete model,
> > > but with solvent channels, the number of disordered electron is not
> > > known, is it?
> > >
> > > Thanks a lot for a clarification!
> > >
> > > Best,
> > > Tim
> > >
> > >
> > > --
> > > --
> > > Tim Gruene
> > > Head of the Centre for X-ray Structure Analysis
> > > Faculty of Chemistry
> > > University of Vienna
> > >
> > > Phone: +43-1-4277-70202
> > >
> > > GPG Key ID = A46BEE1A
> > >
> > >
> 
> > >
> > > To unsubscribe from the COOT list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
> > >
> > > This message was issued to members of www.jiscmail.ac.uk/COOT, a
> > > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> > > available at https://www.jiscmail.ac.uk/policyandsecurity/
> > >
>
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>



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Re: [COOT] absolute map levels

2022-05-02 Thread Tim Gruene
Hi Ian,

this is the custom I was educated with. However, small molecule people
seem confused when a map contour level is described with an rsmd (which
to me makes some sense). When refining a structure with shelxl, the
peak height of the maxima of the difference map corresponds quite well
to the element one is expecting, i.e. the absolute value of the peak
height can be used to guess the missing atom type (e.g. '8' for a
properly ordered oxygen from a water molecule).

Also COOT has been displaying the map countour level with the unit
e/A^3, and I seem to remember Paul's recommendation to use this unit,
rather than the rmsd, which is displayed in brackets.

Cheers,
Tim

On Mon, 2 May 2022 09:48:30 +0100 Ian Tickle  wrote:

> Hi Tim
> 
> F000 is customarily not included in MX electron density for the
> reason you mention.  This doesn't matter because the contour levels
> are completely arbitrary anyway, i.e. you choose a level that shows
> the features you expect to see.  This can be misleading of course
> since there may be significant features at lower density than you
> expected due to thermal motion / disorder or maybe H atoms; however
> including F000 would not change that.
> 
> Cheers
> 
> -- Ian
> 
> 
> On Mon, 2 May 2022 at 07:45, Tim Gruene 
> wrote:
> 
> > Hello readers,
> >
> > how does Coot calculate the absolute map levels, i.e. the contour
> > level given as [e/A^3]? i always thought (rather from hear-say)
> > that F000 was necessary for the absolute level. With a small
> > molecule structure, F000 can be calculated from a complete model,
> > but with solvent channels, the number of disordered electron is not
> > known, is it?
> >
> > Thanks a lot for a clarification!
> >
> > Best,
> > Tim
> >
> >
> > --
> > --
> > Tim Gruene
> > Head of the Centre for X-ray Structure Analysis
> > Faculty of Chemistry
> > University of Vienna
> >
> > Phone: +43-1-4277-70202
> >
> > GPG Key ID = A46BEE1A
> >
> > 
> >
> > To unsubscribe from the COOT list, click the following link:
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-- 
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Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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Re: [COOT] absolute map levels

2022-05-02 Thread Ian Tickle
Hi Tim

F000 is customarily not included in MX electron density for the reason you
mention.  This doesn't matter because the contour levels are completely
arbitrary anyway, i.e. you choose a level that shows the features you
expect to see.  This can be misleading of course since there may be
significant features at lower density than you expected due to thermal
motion / disorder or maybe H atoms; however including F000 would not change
that.

Cheers

-- Ian


On Mon, 2 May 2022 at 07:45, Tim Gruene  wrote:

> Hello readers,
>
> how does Coot calculate the absolute map levels, i.e. the contour level
> given as [e/A^3]? i always thought (rather from hear-say) that F000 was
> necessary for the absolute level. With a small molecule structure, F000
> can be calculated from a complete model, but with solvent channels, the
> number of disordered electron is not known, is it?
>
> Thanks a lot for a clarification!
>
> Best,
> Tim
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
> To unsubscribe from the COOT list, click the following link:
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[COOT] absolute map levels

2022-05-02 Thread Tim Gruene
Hello readers,

how does Coot calculate the absolute map levels, i.e. the contour level
given as [e/A^3]? i always thought (rather from hear-say) that F000 was
necessary for the absolute level. With a small molecule structure, F000
can be calculated from a complete model, but with solvent channels, the
number of disordered electron is not known, is it?

Thanks a lot for a clarification!

Best,
Tim


-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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