Re: [COOT] absolute map levels
I too use the scroll wheel quite a lot when exploring a map. I just like to be grounded by the knowledge of what contour level I'm looking at so I can make estimations of physical interpretations as I'm going. Is this peak likely a Zinc atom? A water molecule? Something at partial occupancy? I can't tell at all from the appearance of the peak, but if I know the contour level on a physically relevant scale (not a statistically relevant scale) I can have a feel for what I'm looking at. I believe that is valuable information to add to that of the surrounding chemical environment and leads me to an interpretation that refinement is likely to support. I find that I'm much less likely to build a Zinc atom into that "strong" difference map peak only to be rewarded with a huge negative peak after refinement because the peak could only support a Zinc at 10% occupancy. Sure, look at your map with a low contour level -- Just be aware that you are looking at a low contoured map. Dale Tronrud On 5/3/2022 6:32 AM, Paul Emsley wrote: On 02/05/2022 20:19, Dale Tronrud wrote: 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. I recall a few years ago that Alex McPherson asked me how I chose the contour level and I said more or less this. He didn't like my answer :-). 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. I don't choose one level and don't recommend that others do so - the continuous re-contouring allow one to get a feel for where the signal descends into noise - so I am scrolling very frequently when deciding where a side-chain should go. I hum the Rawhide theme tune as I do so. Paul. 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/ 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/
Re: [COOT] absolute map levels
Attaching the map contour level to the mouse scroll wheel was one of the most transformative things that Paul did in coot - giving access to the most crucial parameter of map building with an unthinking twitch of the finger. On 03/05/2022 14:32, Paul Emsley wrote: On 02/05/2022 20:19, Dale Tronrud wrote: 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. I recall a few years ago that Alex McPherson asked me how I chose the contour level and I said more or less this. He didn't like my answer :-). 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. I don't choose one level and don't recommend that others do so - the continuous re-contouring allow one to get a feel for where the signal descends into noise - so I am scrolling very frequently when deciding where a side-chain should go. I hum the Rawhide theme tune as I do so. Paul. 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/ 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/
Re: [COOT] absolute map levels
On 02/05/2022 20:19, Dale Tronrud wrote: 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. I recall a few years ago that Alex McPherson asked me how I chose the contour level and I said more or less this. He didn't like my answer :-). 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. I don't choose one level and don't recommend that others do so - the continuous re-contouring allow one to get a feel for where the signal descends into noise - so I am scrolling very frequently when deciding where a side-chain should go. I hum the Rawhide theme tune as I do so. Paul. 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/
Re: [COOT] absolute map levels
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
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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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1
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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
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/
> >
--
--
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
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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Re: [COOT] absolute map levels
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/ pgpLV2QESfPpd.pgp Description: OpenPGP digital signature
Re: [COOT] absolute map levels
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/
Re: [COOT] absolute map levels
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 > https://www.jiscmail.ac.uk/policyandsecurity/ 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/ mime-attachment Description: Binary data
Re: [COOT] absolute map levels
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 > 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/
Re: [COOT] absolute map levels
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 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/ pgpCS9TP9KDNs.pgp Description: OpenPGP digital signature
Re: [COOT] absolute map levels
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/ > 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/
