Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Yao, Sen]

Thanks for the clarification, Pavel! And the article is very helpful as
well.

Cheers,
Sen

On Tue, Mar 5, 2019 at 1:07 PM Pavel Afonine  wrote:

> P.S.: while on the topic, it might be helpful to you to have a look at
> this article ("On the analysis of residual density distributions on an
> absolute scale", page 43) available here:
>
> http://phenix-online.org/newsletter/CCN_2012_07.pdf
>
> Pavel
>
> On Tue, Mar 5, 2019 at 10:02 AM Pavel Afonine  wrote:
>
>> Hi Sen,
>>
>> As Pavel mentioned, phenix.f000 will give you F(0,0,0) value, but I don't
>>> see that information stored and easily calculated from .ccp4 data.
>>>
>>
>>  phenix.f000 requires atomic model (PDB or mmCIF file) as input, not a
>> map. If you want bulk-solvent to be added, then you need to give it mean
>> solvent density.
>>
>> Pavel
>>
>>>

-- 

Sen Yao, PhD
Center for Environmental and Systems Biochemistry/Markey Cancer Center
University of Kentucky, Lexington KY



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Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Pavel Afonine]

P.S.: while on the topic, it might be helpful to you to have a look at this
article ("On the analysis of residual density distributions on an absolute
scale", page 43) available here:

http://phenix-online.org/newsletter/CCN_2012_07.pdf

Pavel

On Tue, Mar 5, 2019 at 10:02 AM Pavel Afonine  wrote:

> Hi Sen,
>
> As Pavel mentioned, phenix.f000 will give you F(0,0,0) value, but I don't
>> see that information stored and easily calculated from .ccp4 data.
>>
>
>  phenix.f000 requires atomic model (PDB or mmCIF file) as input, not a
> map. If you want bulk-solvent to be added, then you need to give it mean
> solvent density.
>
> Pavel
>
>>



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Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Pavel Afonine]

Hi Sen,

As Pavel mentioned, phenix.f000 will give you F(0,0,0) value, but I don't
> see that information stored and easily calculated from .ccp4 data.
>

 phenix.f000 requires atomic model (PDB or mmCIF file) as input, not a map.
If you want bulk-solvent to be added, then you need to give it mean solvent
density.

Pavel

>



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Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Gerard Bricogne]

Dear Sen,

 Our messages just crossed ... .

 With best wishes,

  Gerard.
--
On Tue, Mar 05, 2019 at 11:32:01AM -0500, Yao, Sen wrote:
> Dear Gerard,
> 
> Thank you for your reply. I totally agree with you.
> 
> The average value of the 2mFo-DFc map should be zero, and from my
> observation, most of them are a very small number (<0.001) that can be
> viewed as zero practically. As Pavel mentioned, phenix.f000 will give you
> F(0,0,0) value, but I don't see that information stored and easily
> calculated from .ccp4 data.
> 
> Your solution to add up the electrons in the model and divide by the number
> of voxels related to the model is in essence what I did to aggregate the
> atoms into chains. The problem is determining the voxels to include which
> require the radii determined for each atoms. For that I optimized the radii
> for each atom type using the criteria that all atoms need to include a
> significant number of electrons and give a consistent result across the
> whole PDB structures.
> 
> And with all that, I got this ~1/3 value of the theoretical number of
> electrons. I guess what I have to do is to use this ratio and convert them
> back to an actual number of electron meaning.
> 
> Thank you all for the input!
> 
> Cheers,
> Sen
> 
> 
> On Mon, Mar 4, 2019 at 1:21 PM Gerard Bricogne 
> wrote:
> 
> > Dear Sen,
> >
> >  I may be unaware of special features of these maps, but if they
> > are computed in conventional ways, they lack an F000 term. Therefore
> > the average value of the 2mFo-DFc map is zero, just as if it was a
> > difference map. This may explain why you do not find all the electrons
> > you would be expecting. To get this right, you would need to add that
> > F000 term to the set of Fourier coefficients going into the
> > calculation of the map. You can get a pretty satisfactory F000 value
> > by taking it from the Fourier transform of the model density, and
> > applying the appropriate scale factor. Unfortunately not all structure
> > factor programs will give you that F000. Instead, then, you can add
> > the numbers of electrons for all the atoms of your model in the unit
> > cell, put it on "map scale", divide it by the number of voxels in that
> > unit cell, and add it to all the map values in all the voxels you
> > examine.
> >
> >  In any case, the use of a zero-mean map would be the cause of
> > your 1/3 factor.
> >
> >  Apologies to the PDBe if they have already thought of that and
> > are including the F000 (or average number of electrons per voxel) into
> > the calculation of their maps - I didn't see any sign that this was
> > being done.
> >
> >
> >  With best wishes,
> >
> >   Gerard.
> >
> > --
> > On Mon, Mar 04, 2019 at 10:36:11AM -0500, Yao, Sen wrote:
> > > Hi all,
> > >
> > > I have been using the electron density maps available on the PDBe website
> > > to run some analysis. And I run into this question that I hope that I can
> > > get some help from the community.
> > >
> > > In the ccp4 format, the electron density is represented as a 3-d array
> > map,
> > > with each number corresponds to the density value of a voxel in real
> > space.
> > > If I add all voxel densities around an atom together and divided it by
> > the
> > > number of electrons of that atom, in theory it should give me a ratio
> > with
> > > the unit Å-3 (angstrom to the power of -3), and this ratio should be
> > > inversely related to the voxel volume. (Correct me if I am wrong here.)
> > > However, after I got this ratio for each atom, aggregated it into chains
> > > and calculated a median, and then compared the chain median to the voxel
> > > volume over all PDB structures with electron density available, they
> > show a
> > > slope of ~1/3 instead of expected 1 (see attached link). That is, almost
> > > all the values in the electron density maps are only about 1/3 of
> > > represented electrons.
> > >
> > >
> > https://drive.google.com/file/d/1K_3uxZfUPuTdH1DtKJgKHLRUA5NHTVPB/view?usp=sharing
> > >
> > >
> > > So my question is, is there a conversion or scaling factor that PDBe uses
> > > to generate the ccp4 files? If so, is that information stored in the ccp4
> > > files or anywhere else? And if not, why do I observe this 1/3 ratio
> > pretty
> > > consistently across the whole PDB?
> > >
> > > I would really appreciate any insights on this matter. Thank you!
> > >
> > > Sincerely,
> > > Sen
> > >
> > > --
> > >
> > > Sen Yao, PhD
> > > Center for Environmental and Systems Biochemistry
> > > Markey Cancer Center
> > > University of Kentucky, Lexington KY
> > >
> > > 
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >
> > --
> >
> >  ===
> >  * *
> > 

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Gerard Bricogne]

Dear Sen

On Tue, Mar 05, 2019 at 11:05:26AM -0500, Yao, Sen wrote:
> Thank you Ian! The response is really informative.
> 
> I am aware that electron density is a point sample. And multiply it by the
> voxel volume is an estimated average. I do have a normalization step in my
> calculation that should average this potential error out. It would be nice
> to sample it finely, but given that I am working with just the ccp4 files
> available, how they sampled it is what went directly in my calculations.
> Hope this clarifies your concerns.
> 
> For the second issue, I've also notice that as well and did actually
> optimize the radii for each atom type based on the criteria that they need
> to include a significant number of electrons across the whole PDB
> structures. Voronoi polyhedra is probably another way to do it; as for my
> calculation, I think once the density is below 1.5 sigma (for 2mFo-DFc),
> there is not much information gain to keep extending the radii around an
> atom.

 The term "1.5 sigma" says it all: this "sigma" a root-mean-square
deviation from the average density in the map, which is zero because
of the absence of the F000 term in the Fourier synthesis used to
compute that map. To get the pointwise density you want, you have to
add back that missing true mean density per voxel, i.e. on absolute
scale the total number of electrons in the unit cell divided by the
number of voxels in that unit cell.

> And for the first issue you mentioned, it is a very interesting point. I
> don't have anything to directly correct for that on an atom level. But I do
> aggregate atoms into chains (sum of all density together of all atoms on a
> chain and divide by the total number of voxels involved). Maybe that will
> account for potential atomic misplacement? But for the density being only
> part of the true density, I am not sure there is an easy way to account for
> that from ccp4 data only.
> 
> Best,
> Sen
> 
> 
> On Mon, Mar 4, 2019 at 12:43 PM Ian Tickle  wrote:
> 
> >
> > Hi Sen
> >
> > If you multiply the electron density in a voxel by the voxel volume you
> > should get an estimate of the number of electrons contained in that voxel,
> > and then you can add up the numbers of electrons in all the voxels occupied
> > by an atom to get the total number of electrons in that atom, which is
> > basically the same as what you are saying.
> >
> > However note that the electron density is a point sample: it's not the
> > average density in the voxel, so the above calculation won't be quite
> > accurate, depending on the 'smoothness' of the density.  This is like the
> > error in an integral by use of Simpson's rule.  To be sure of accounting
> > for all the density you need to sample it finely, say not more that Dmin/4.
> >
> > There are two more issues here: first the atomic positions are never
> > error-free which reduces the contribution to the density by the factor D in
> > the expression 2mFo-DFc (or mFo for centric phases) for the map
> > coefficients.  So if the errors were sufficiently large D would tend to
> > zero and you would get no density at all!  The density that you see is
> > really only that part of the true density for which there is evidence in
> > the experimental data.
> >
> > Second, what exactly do you mean by "add all voxel densities around an
> > atom"?  The electron density could easily extend 2 Ang. from an atomic
> > centre, depending on the atom's finite size (represented by the form
> > factor), its thermal motion (B factor) and series termination effects
> > (resolution).  So if you don't go out far enough you will fail to account
> > for some fraction of the electron count.  The problem is of course you
> > can't go so far as to overlap bonded atoms which will be well within 2 Ang.
> > distance.  The standard method of dealing with this is to represent 'soft'
> > atoms (where the distance between atoms may be less than the sum of their
> > radii) as Voronoi polyhedra (like the packing of soap bubbles!).  Is that
> > how you handled it?
> >
> > Cheers
> >
> > -- Ian
> >
> >
> > On Mon, 4 Mar 2019 at 15:47, Yao, Sen  wrote:
> >
> >> Hi all,
> >>
> >> I have been using the electron density maps available on the PDBe website
> >> to run some analysis. And I run into this question that I hope that I can
> >> get some help from the community.
> >>
> >> In the ccp4 format, the electron density is represented as a 3-d array
> >> map, with each number corresponds to the density value of a voxel in real
> >> space. If I add all voxel densities around an atom together and divided it
> >> by the number of electrons of that atom, in theory it should give me a
> >> ratio with the unit Å-3 (angstrom to the power of -3), and this ratio
> >> should be inversely related to the voxel volume. (Correct me if I am wrong
> >> here.) However, after I got this ratio for each atom, aggregated it into
> >> chains and calculated a median, and then compared the chain median to the
> >> voxel volum

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Yao, Sen]

Dear Gerard,

Thank you for your reply. I totally agree with you.

The average value of the 2mFo-DFc map should be zero, and from my
observation, most of them are a very small number (<0.001) that can be
viewed as zero practically. As Pavel mentioned, phenix.f000 will give you
F(0,0,0) value, but I don't see that information stored and easily
calculated from .ccp4 data.

Your solution to add up the electrons in the model and divide by the number
of voxels related to the model is in essence what I did to aggregate the
atoms into chains. The problem is determining the voxels to include which
require the radii determined for each atoms. For that I optimized the radii
for each atom type using the criteria that all atoms need to include a
significant number of electrons and give a consistent result across the
whole PDB structures.

And with all that, I got this ~1/3 value of the theoretical number of
electrons. I guess what I have to do is to use this ratio and convert them
back to an actual number of electron meaning.

Thank you all for the input!

Cheers,
Sen


On Mon, Mar 4, 2019 at 1:21 PM Gerard Bricogne 
wrote:

> Dear Sen,
>
>  I may be unaware of special features of these maps, but if they
> are computed in conventional ways, they lack an F000 term. Therefore
> the average value of the 2mFo-DFc map is zero, just as if it was a
> difference map. This may explain why you do not find all the electrons
> you would be expecting. To get this right, you would need to add that
> F000 term to the set of Fourier coefficients going into the
> calculation of the map. You can get a pretty satisfactory F000 value
> by taking it from the Fourier transform of the model density, and
> applying the appropriate scale factor. Unfortunately not all structure
> factor programs will give you that F000. Instead, then, you can add
> the numbers of electrons for all the atoms of your model in the unit
> cell, put it on "map scale", divide it by the number of voxels in that
> unit cell, and add it to all the map values in all the voxels you
> examine.
>
>  In any case, the use of a zero-mean map would be the cause of
> your 1/3 factor.
>
>  Apologies to the PDBe if they have already thought of that and
> are including the F000 (or average number of electrons per voxel) into
> the calculation of their maps - I didn't see any sign that this was
> being done.
>
>
>  With best wishes,
>
>   Gerard.
>
> --
> On Mon, Mar 04, 2019 at 10:36:11AM -0500, Yao, Sen wrote:
> > Hi all,
> >
> > I have been using the electron density maps available on the PDBe website
> > to run some analysis. And I run into this question that I hope that I can
> > get some help from the community.
> >
> > In the ccp4 format, the electron density is represented as a 3-d array
> map,
> > with each number corresponds to the density value of a voxel in real
> space.
> > If I add all voxel densities around an atom together and divided it by
> the
> > number of electrons of that atom, in theory it should give me a ratio
> with
> > the unit Å-3 (angstrom to the power of -3), and this ratio should be
> > inversely related to the voxel volume. (Correct me if I am wrong here.)
> > However, after I got this ratio for each atom, aggregated it into chains
> > and calculated a median, and then compared the chain median to the voxel
> > volume over all PDB structures with electron density available, they
> show a
> > slope of ~1/3 instead of expected 1 (see attached link). That is, almost
> > all the values in the electron density maps are only about 1/3 of
> > represented electrons.
> >
> >
> https://drive.google.com/file/d/1K_3uxZfUPuTdH1DtKJgKHLRUA5NHTVPB/view?usp=sharing
> >
> >
> > So my question is, is there a conversion or scaling factor that PDBe uses
> > to generate the ccp4 files? If so, is that information stored in the ccp4
> > files or anywhere else? And if not, why do I observe this 1/3 ratio
> pretty
> > consistently across the whole PDB?
> >
> > I would really appreciate any insights on this matter. Thank you!
> >
> > Sincerely,
> > Sen
> >
> > --
> >
> > Sen Yao, PhD
> > Center for Environmental and Systems Biochemistry
> > Markey Cancer Center
> > University of Kentucky, Lexington KY
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> --
>
>  ===
>  * *
>  * Gerard Bricogne g...@globalphasing.com  *
>  * *
>  * Global Phasing Ltd. *
>  * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
>  * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
>  * 

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Pavel Afonine]

Hi,


> Unfortunately not all structure
> factor programs will give you that F000.
>

phenix.f000 will give you F(0,0,0) value based on atomic model alone or
atomic model plus bulk-solvent.

Pavel



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Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Edward A. Berry]

Also check if the mean value of the map over the ASU is zero. If so, the map 
was probably calculated without the 0,0,0 term of the Fourier series, so zero 
does not represent zero density but rather the mean density.

On 03/04/2019 12:43 PM, Ian Tickle wrote:


Hi Sen

If you multiply the electron density in a voxel by the voxel volume you should 
get an estimate of the number of electrons contained in that voxel, and then 
you can add up the numbers of electrons in all the voxels occupied by an atom 
to get the total number of electrons in that atom, which is basically the same 
as what you are saying.

However note that the electron density is a point sample: it's not the average 
density in the voxel, so the above calculation won't be quite accurate, 
depending on the 'smoothness' of the density.  This is like the error in an 
integral by use of Simpson's rule.  To be sure of accounting for all the 
density you need to sample it finely, say not more that Dmin/4.

There are two more issues here: first the atomic positions are never error-free 
which reduces the contribution to the density by the factor D in the expression 
2mFo-DFc (or mFo for centric phases) for the map coefficients.  So if the 
errors were sufficiently large D would tend to zero and you would get no 
density at all!  The density that you see is really only that part of the true 
density for which there is evidence in the experimental data.

Second, what exactly do you mean by "add all voxel densities around an atom"?  
The electron density could easily extend 2 Ang. from an atomic centre, depending on the 
atom's finite size (represented by the form factor), its thermal motion (B factor) and 
series termination effects (resolution).  So if you don't go out far enough you will fail 
to account for some fraction of the electron count.  The problem is of course you can't 
go so far as to overlap bonded atoms which will be well within 2 Ang. distance.  The 
standard method of dealing with this is to represent 'soft' atoms (where the distance 
between atoms may be less than the sum of their radii) as Voronoi polyhedra (like the 
packing of soap bubbles!).  Is that how you handled it?

Cheers

-- Ian


On Mon, 4 Mar 2019 at 15:47, Yao, Sen mailto:yaosen1...@gmail.com>> wrote:

Hi all,

I have been using the electron density maps available on the PDBe website 
to run some analysis. And I run into this question that I hope that I can get 
some help from the community.

In the ccp4 format, the electron density is represented as a 3-d array map, 
with each number corresponds to the density value of a voxel in real space. If 
I add all voxel densities around an atom together and divided it by the number 
of electrons of that atom, in theory it should give me a ratio with the unit 
Å-3 (angstrom to the power of -3), and this ratio should be inversely related 
to the voxel volume. (Correct me if I am wrong here.) However, after I got this 
ratio for each atom, aggregated it into chains and calculated a median, and 
then compared the chain median to the voxel volume over all PDB structures with 
electron density available, they show a slope of ~1/3 instead of expected 1 
(see attached link). That is, almost all the values in the electron density 
maps are only about 1/3 of represented electrons.

https://drive.google.com/file/d/1K_3uxZfUPuTdH1DtKJgKHLRUA5NHTVPB/view?usp=sharing 



So my question is, is there a conversion or scaling factor that PDBe uses 
to generate the ccp4 files? If so, is that information stored in the ccp4 files 
or anywhere else? And if not, why do I observe this 1/3 ratio pretty 
consistently across the whole PDB?

I would really appreciate any insights on this matter. Thank you!

Sincerely,
Sen

--

Sen Yao, PhD

Center for Environmental and Systems Biochemistry
Markey Cancer Center
University of Kentucky, Lexington KY

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Gerard Bricogne]

Dear Sen,

 I may be unaware of special features of these maps, but if they
are computed in conventional ways, they lack an F000 term. Therefore
the average value of the 2mFo-DFc map is zero, just as if it was a
difference map. This may explain why you do not find all the electrons
you would be expecting. To get this right, you would need to add that
F000 term to the set of Fourier coefficients going into the
calculation of the map. You can get a pretty satisfactory F000 value
by taking it from the Fourier transform of the model density, and
applying the appropriate scale factor. Unfortunately not all structure
factor programs will give you that F000. Instead, then, you can add
the numbers of electrons for all the atoms of your model in the unit
cell, put it on "map scale", divide it by the number of voxels in that
unit cell, and add it to all the map values in all the voxels you
examine.

 In any case, the use of a zero-mean map would be the cause of
your 1/3 factor. 

 Apologies to the PDBe if they have already thought of that and
are including the F000 (or average number of electrons per voxel) into
the calculation of their maps - I didn't see any sign that this was
being done.


 With best wishes,

  Gerard.

--
On Mon, Mar 04, 2019 at 10:36:11AM -0500, Yao, Sen wrote:
> Hi all,
> 
> I have been using the electron density maps available on the PDBe website
> to run some analysis. And I run into this question that I hope that I can
> get some help from the community.
> 
> In the ccp4 format, the electron density is represented as a 3-d array map,
> with each number corresponds to the density value of a voxel in real space.
> If I add all voxel densities around an atom together and divided it by the
> number of electrons of that atom, in theory it should give me a ratio with
> the unit Å-3 (angstrom to the power of -3), and this ratio should be
> inversely related to the voxel volume. (Correct me if I am wrong here.)
> However, after I got this ratio for each atom, aggregated it into chains
> and calculated a median, and then compared the chain median to the voxel
> volume over all PDB structures with electron density available, they show a
> slope of ~1/3 instead of expected 1 (see attached link). That is, almost
> all the values in the electron density maps are only about 1/3 of
> represented electrons.
> 
> https://drive.google.com/file/d/1K_3uxZfUPuTdH1DtKJgKHLRUA5NHTVPB/view?usp=sharing
> 
> 
> So my question is, is there a conversion or scaling factor that PDBe uses
> to generate the ccp4 files? If so, is that information stored in the ccp4
> files or anywhere else? And if not, why do I observe this 1/3 ratio pretty
> consistently across the whole PDB?
> 
> I would really appreciate any insights on this matter. Thank you!
> 
> Sincerely,
> Sen
> 
> -- 
> 
> Sen Yao, PhD
> Center for Environmental and Systems Biochemistry
> Markey Cancer Center
> University of Kentucky, Lexington KY
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

-- 

 ===
 * *
 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===



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https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] Question about the electron density maps (.ccp4) in PDBe

[Yao, Sen]

Hi all,

I have been using the electron density maps available on the PDBe website
to run some analysis. And I run into this question that I hope that I can
get some help from the community.

In the ccp4 format, the electron density is represented as a 3-d array map,
with each number corresponds to the density value of a voxel in real space.
If I add all voxel densities around an atom together and divided it by the
number of electrons of that atom, in theory it should give me a ratio with
the unit Å-3 (angstrom to the power of -3), and this ratio should be
inversely related to the voxel volume. (Correct me if I am wrong here.)
However, after I got this ratio for each atom, aggregated it into chains
and calculated a median, and then compared the chain median to the voxel
volume over all PDB structures with electron density available, they show a
slope of ~1/3 instead of expected 1 (see attached link). That is, almost
all the values in the electron density maps are only about 1/3 of
represented electrons.

https://drive.google.com/file/d/1K_3uxZfUPuTdH1DtKJgKHLRUA5NHTVPB/view?usp=sharing


So my question is, is there a conversion or scaling factor that PDBe uses
to generate the ccp4 files? If so, is that information stored in the ccp4
files or anywhere else? And if not, why do I observe this 1/3 ratio pretty
consistently across the whole PDB?

I would really appreciate any insights on this matter. Thank you!

Sincerely,
Sen

-- 

Sen Yao, PhD
Center for Environmental and Systems Biochemistry
Markey Cancer Center
University of Kentucky, Lexington KY



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1