Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

[Dale Tronrud]

   I agree completely!  The higher resolution data is determined
entirely by the atoms with low B factor.  If fact, the Wilson B plots
I've seen have a distinct curve to them -- They are not straight lines.
 As one looks to higher and higher resolution the curve gets shallower
and shallower.  You can actually see the population of atoms
contributing to each increasing resolution has a lower and lower average B.

Dale Tronrud

On 3/12/2019 2:24 PM, Edward A. Berry wrote:
> What if you have one domain with many B-factors aroun 70 and above, and
> another domain with B-factors around 20? The atoms with high B-factor
> will make essentially no contribution to the intensty of spots beyond 3
> A, and so have no effect on the slope of the Wilson plot byond that. But
> they will contribute mightily to the average atomic B. Or so it seems to
> me.
> eab
> 
> On 03/12/2019 04:39 PM, DUMAS Philippe (IGBMC) wrote:
>>
>> Le Mardi 12 Mars 2019 19:55 CET, Dale Tronrud 
>> a écrit:
>>
>> Dale
>> Good to have the opportunity of going back to the crystallography of
>> the fifties in these post-modern times...
>> There is an essential argumentation that should be recalled. The only
>> reason for the fact that one ignores low-resolution data in a Wilson
>> plot is that a Wilson plot is based precisely upon Wilson statistics,
>> which assumes that the atoms are cast randomly in the unit cell.
>> This assumption obviously does not hold at low resolution and there is
>> no reason to obtain a straight line that stems from the latter
>> assumption.
>> Therefore, I do not think one may say that a Wilson plot tends to
>> ignore atoms with high B values.
>> Consequence: if one has data at rather low resolution, a Wilson plot
>> is inherently inaccurate, but if one has data at very high resolution,
>> the Wilson plot should give a very decent estimate of the average B
>> and any significant discrepancy should ring the bell.
>> Philippe Dumas
>>
>>
>>>     The numeric average of the B factors of the atoms in your model only
>>> roughly corresponds to the calculation of the Wilson B.  While I always
>>> expect the average B to be larger than the Wilson B, how much larger
>>
>>> depends on many factors, making it a fairly useless criteria for judging
>>> the correctness of a model.
>>>
>>>     While it is pretty easy to understand the average of the B
>>> factors in
>>> your model, the Wilson B is more difficult.  Since it is calculated by
>>> drawing a line though the (Log of) the intensity of your structure
>>> factors as a function of the square of sin theta over lambda, it is
>>> rather removed from the atomic B factors.  When drawing the line the low
>>> resolution data are ignored because those data don't fall on a straight
>>> line, and this means that the large B factor atoms in your model are
>>
>>> ignored in the Wilson B calculation.
>>>
>>>     The Wilson B is (sort of) a weighted average of the B factors of
>>> your
>>> model, with the smallest B's given the largest weight.  The actually
>>
>>> weighting factor is a little obscure so I don't know how to simulate it
>>> to adjust the averaging of atomic B's to come out a match.  The easiest
>>> way to compare your model to the Wilson B is to calculate structure
>>> factors from it and calculate the Calculated Wilson B.  No one does this
>>> because it will always come out as a match.  If your calculated Wilson B
>>> doesn't match the observed Wilson B your R values are guaranteed to be
>>> unacceptable and your refinement program will have to be malfunctioning
>>> to create such a model.
>>>
>>>     If all the B factors in your model are equal to each other, your
>>> refined model will have an average B that matches the Wilson B, because
>>> weighting doesn't matter in that situation.  If you allow the B's to
>>
>>> vary, the difference between the average and the Wilson B will depend on
>>> how high of an individual B factor you are willing to tolerate.  If you
>>> are a person who likes to build chain into weak loops of density, or
>>
>>> build side chains where there is little to no density, then your average
>>> B will be much larger than the Wilson B.  This does not mean there is an
>>> error, it is simply a reflection of the Wilson B's insensitivity to
>>> atoms with large B.
>>>
>>>     I do not believe comparing the average B to the Wilson B has any
>>> utility at all.
>>>
>>> Dale Tronrud
>>>
>>> On 3/12/2019 11:34 AM, Eze Chivi wrote:
 Dear CCP4bb community,


 The average B-factor (calculated from model) of my protein is 65,
 whereas the Wilson B is 52. I have read in this BB that "it is expected
 that average B does not deviate strongly from the Wilson B". How I can
 evaluate if the difference calculated for my data is razonable or not?


 Thank you in advance


 Ezequiel


 


 To unsubscribe from the CCP4BB list, 

Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

[Ian Tickle]

Hi Edward

This is because taking a naive straight arithmetic average of the B factors
as all the programs do is nonsense!  To simplify your argument say we have
just 2 atoms with B = 10 and 1000.  What's the average B?  Answer: not 505
but very close to 10 because the atom with B=1000 most likely isn't there.
So you need an average weighted by the contribution to the scattering over
the resolution range.  This is effectively what the Wilson plot is doing:
it is certainly not performing a naive arithmetic average.  So if you're
going to compare it, at least compare it with the right quantity, though
I'm not claiming that this will give you better agreement between the
weighted average & Wilson Bs, for reasons mentioned by others.

For a possible solution see: Acta Cryst. 
 (1998). D*54* , 243-252
(shameless plug).

Cheers

-- Ian

On Tue, 12 Mar 2019 at 21:24, Edward A. Berry  wrote:

> What if you have one domain with many B-factors aroun 70 and above, and
> another domain with B-factors around 20? The atoms with high B-factor will
> make essentially no contribution to the intensty of spots beyond 3 A, and
> so have no effect on the slope of the Wilson plot byond that. But they will
> contribute mightily to the average atomic B. Or so it seems to me.
> eab
>
> On 03/12/2019 04:39 PM, DUMAS Philippe (IGBMC) wrote:
> >
> > Le Mardi 12 Mars 2019 19:55 CET, Dale Tronrud  a
> écrit:
> >
> > Dale
> > Good to have the opportunity of going back to the crystallography of the
> fifties in these post-modern times...
> > There is an essential argumentation that should be recalled. The only
> reason for the fact that one ignores low-resolution data in a Wilson plot
> is that a Wilson plot is based precisely upon Wilson statistics, which
> assumes that the atoms are cast randomly in the unit cell.
> > This assumption obviously does not hold at low resolution and there is
> no reason to obtain a straight line that stems from the latter assumption.
> > Therefore, I do not think one may say that a Wilson plot tends to ignore
> atoms with high B values.
> > Consequence: if one has data at rather low resolution, a Wilson plot is
> inherently inaccurate, but if one has data at very high resolution, the
> Wilson plot should give a very decent estimate of the average B and any
> significant discrepancy should ring the bell.
> > Philippe Dumas
> >
> >
> >> The numeric average of the B factors of the atoms in your model only
> >> roughly corresponds to the calculation of the Wilson B.  While I always
> >> expect the average B to be larger than the Wilson B, how much larger
> >
> >> depends on many factors, making it a fairly useless criteria for judging
> >> the correctness of a model.
> >>
> >> While it is pretty easy to understand the average of the B factors
> in
> >> your model, the Wilson B is more difficult.  Since it is calculated by
> >> drawing a line though the (Log of) the intensity of your structure
> >> factors as a function of the square of sin theta over lambda, it is
> >> rather removed from the atomic B factors.  When drawing the line the low
> >> resolution data are ignored because those data don't fall on a straight
> >> line, and this means that the large B factor atoms in your model are
> >
> >> ignored in the Wilson B calculation.
> >>
> >> The Wilson B is (sort of) a weighted average of the B factors of
> your
> >> model, with the smallest B's given the largest weight.  The actually
> >
> >> weighting factor is a little obscure so I don't know how to simulate it
> >> to adjust the averaging of atomic B's to come out a match.  The easiest
> >> way to compare your model to the Wilson B is to calculate structure
> >> factors from it and calculate the Calculated Wilson B.  No one does this
> >> because it will always come out as a match.  If your calculated Wilson B
> >> doesn't match the observed Wilson B your R values are guaranteed to be
> >> unacceptable and your refinement program will have to be malfunctioning
> >> to create such a model.
> >>
> >> If all the B factors in your model are equal to each other, your
> >> refined model will have an average B that matches the Wilson B, because
> >> weighting doesn't matter in that situation.  If you allow the B's to
> >
> >> vary, the difference between the average and the Wilson B will depend on
> >> how high of an individual B factor you are willing to tolerate.  If you
> >> are a person who likes to build chain into weak loops of density, or
> >
> >> build side chains where there is little to no density, then your average
> >> B will be much larger than the Wilson B.  This does not mean there is an
> >> error, it is simply a reflection of the Wilson B's insensitivity to
> >> atoms with large B.
> >>
> >> I do not believe comparing the average B to the Wilson B has any
> >> utility at all.
> >>
> >> Dale Tronrud
> >>
> >> On 3/12/2019 11:34 AM, Eze Chivi 

Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

[Edward A. Berry]

What if you have one domain with many B-factors aroun 70 and above, and another 
domain with B-factors around 20? The atoms with high B-factor will make 
essentially no contribution to the intensty of spots beyond 3 A, and so have no 
effect on the slope of the Wilson plot byond that. But they will contribute 
mightily to the average atomic B. Or so it seems to me.
eab

On 03/12/2019 04:39 PM, DUMAS Philippe (IGBMC) wrote:


Le Mardi 12 Mars 2019 19:55 CET, Dale Tronrud  a écrit:

Dale
Good to have the opportunity of going back to the crystallography of the 
fifties in these post-modern times...
There is an essential argumentation that should be recalled. The only reason 
for the fact that one ignores low-resolution data in a Wilson plot is that a 
Wilson plot is based precisely upon Wilson statistics, which assumes that the 
atoms are cast randomly in the unit cell.
This assumption obviously does not hold at low resolution and there is no 
reason to obtain a straight line that stems from the latter assumption.
Therefore, I do not think one may say that a Wilson plot tends to ignore atoms 
with high B values.
Consequence: if one has data at rather low resolution, a Wilson plot is 
inherently inaccurate, but if one has data at very high resolution, the Wilson 
plot should give a very decent estimate of the average B and any significant 
discrepancy should ring the bell.
Philippe Dumas



The numeric average of the B factors of the atoms in your model only
roughly corresponds to the calculation of the Wilson B.  While I always
expect the average B to be larger than the Wilson B, how much larger



depends on many factors, making it a fairly useless criteria for judging
the correctness of a model.

While it is pretty easy to understand the average of the B factors in
your model, the Wilson B is more difficult.  Since it is calculated by
drawing a line though the (Log of) the intensity of your structure
factors as a function of the square of sin theta over lambda, it is
rather removed from the atomic B factors.  When drawing the line the low
resolution data are ignored because those data don't fall on a straight
line, and this means that the large B factor atoms in your model are



ignored in the Wilson B calculation.

The Wilson B is (sort of) a weighted average of the B factors of your
model, with the smallest B's given the largest weight.  The actually



weighting factor is a little obscure so I don't know how to simulate it
to adjust the averaging of atomic B's to come out a match.  The easiest
way to compare your model to the Wilson B is to calculate structure
factors from it and calculate the Calculated Wilson B.  No one does this
because it will always come out as a match.  If your calculated Wilson B
doesn't match the observed Wilson B your R values are guaranteed to be
unacceptable and your refinement program will have to be malfunctioning
to create such a model.

If all the B factors in your model are equal to each other, your
refined model will have an average B that matches the Wilson B, because
weighting doesn't matter in that situation.  If you allow the B's to



vary, the difference between the average and the Wilson B will depend on
how high of an individual B factor you are willing to tolerate.  If you
are a person who likes to build chain into weak loops of density, or



build side chains where there is little to no density, then your average
B will be much larger than the Wilson B.  This does not mean there is an
error, it is simply a reflection of the Wilson B's insensitivity to
atoms with large B.

I do not believe comparing the average B to the Wilson B has any
utility at all.

Dale Tronrud

On 3/12/2019 11:34 AM, Eze Chivi wrote:

Dear CCP4bb community,


The average B-factor (calculated from model) of my protein is 65,
whereas the Wilson B is 52. I have read in this BB that "it is expected
that average B does not deviate strongly from the Wilson B". How I can
evaluate if the difference calculated for my data is razonable or not?


Thank you in advance


Ezequiel




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Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

[IGBMC]

Le Mardi 12 Mars 2019 19:55 CET, Dale Tronrud  a écrit:

Dale
Good to have the opportunity of going back to the crystallography of the 
fifties in these post-modern times...
There is an essential argumentation that should be recalled. The only reason 
for the fact that one ignores low-resolution data in a Wilson plot is that a 
Wilson plot is based precisely upon Wilson statistics, which assumes that the 
atoms are cast randomly in the unit cell.
This assumption obviously does not hold at low resolution and there is no 
reason to obtain a straight line that stems from the latter assumption.
Therefore, I do not think one may say that a Wilson plot tends to ignore atoms 
with high B values.
Consequence: if one has data at rather low resolution, a Wilson plot is 
inherently inaccurate, but if one has data at very high resolution, the Wilson 
plot should give a very decent estimate of the average B and any significant 
discrepancy should ring the bell.
Philippe Dumas


>The numeric average of the B factors of the atoms in your model only
> roughly corresponds to the calculation of the Wilson B.  While I always
> expect the average B to be larger than the Wilson B, how much larger

> depends on many factors, making it a fairly useless criteria for judging
> the correctness of a model.
>
>While it is pretty easy to understand the average of the B factors in
> your model, the Wilson B is more difficult.  Since it is calculated by
> drawing a line though the (Log of) the intensity of your structure
> factors as a function of the square of sin theta over lambda, it is
> rather removed from the atomic B factors.  When drawing the line the low
> resolution data are ignored because those data don't fall on a straight
> line, and this means that the large B factor atoms in your model are

> ignored in the Wilson B calculation.
>
>The Wilson B is (sort of) a weighted average of the B factors of your
> model, with the smallest B's given the largest weight.  The actually

> weighting factor is a little obscure so I don't know how to simulate it
> to adjust the averaging of atomic B's to come out a match.  The easiest
> way to compare your model to the Wilson B is to calculate structure
> factors from it and calculate the Calculated Wilson B.  No one does this
> because it will always come out as a match.  If your calculated Wilson B
> doesn't match the observed Wilson B your R values are guaranteed to be
> unacceptable and your refinement program will have to be malfunctioning
> to create such a model.
>
>If all the B factors in your model are equal to each other, your
> refined model will have an average B that matches the Wilson B, because
> weighting doesn't matter in that situation.  If you allow the B's to

> vary, the difference between the average and the Wilson B will depend on
> how high of an individual B factor you are willing to tolerate.  If you
> are a person who likes to build chain into weak loops of density, or

> build side chains where there is little to no density, then your average
> B will be much larger than the Wilson B.  This does not mean there is an
> error, it is simply a reflection of the Wilson B's insensitivity to
> atoms with large B.
>
>I do not believe comparing the average B to the Wilson B has any
> utility at all.
>
> Dale Tronrud
>
> On 3/12/2019 11:34 AM, Eze Chivi wrote:
> > Dear CCP4bb community,
> >
> >
> > The average B-factor (calculated from model) of my protein is 65,
> > whereas the Wilson B is 52. I have read in this BB that "it is expected
> > that average B does not deviate strongly from the Wilson B". How I can
> > evaluate if the difference calculated for my data is razonable or not?
> >
> >
> > Thank you in advance
> >
> >
> > Ezequiel
> >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1







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Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

[Diana Tomchick]

>   I do not believe comparing the average B to the Wilson B has any
> utility at all.
>
> Dale Tronrud

There are not many times that reading a CCP4bb posting makes me laugh out loud, 
but this one made my day. Thanks!

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)




UT Southwestern


Medical Center



The future of medicine, today.



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Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

[Dale Tronrud]

   The numeric average of the B factors of the atoms in your model only
roughly corresponds to the calculation of the Wilson B.  While I always
expect the average B to be larger than the Wilson B, how much larger
depends on many factors, making it a fairly useless criteria for judging
the correctness of a model.

   While it is pretty easy to understand the average of the B factors in
your model, the Wilson B is more difficult.  Since it is calculated by
drawing a line though the (Log of) the intensity of your structure
factors as a function of the square of sin theta over lambda, it is
rather removed from the atomic B factors.  When drawing the line the low
resolution data are ignored because those data don't fall on a straight
line, and this means that the large B factor atoms in your model are
ignored in the Wilson B calculation.

   The Wilson B is (sort of) a weighted average of the B factors of your
model, with the smallest B's given the largest weight.  The actually
weighting factor is a little obscure so I don't know how to simulate it
to adjust the averaging of atomic B's to come out a match.  The easiest
way to compare your model to the Wilson B is to calculate structure
factors from it and calculate the Calculated Wilson B.  No one does this
because it will always come out as a match.  If your calculated Wilson B
doesn't match the observed Wilson B your R values are guaranteed to be
unacceptable and your refinement program will have to be malfunctioning
to create such a model.

   If all the B factors in your model are equal to each other, your
refined model will have an average B that matches the Wilson B, because
weighting doesn't matter in that situation.  If you allow the B's to
vary, the difference between the average and the Wilson B will depend on
how high of an individual B factor you are willing to tolerate.  If you
are a person who likes to build chain into weak loops of density, or
build side chains where there is little to no density, then your average
B will be much larger than the Wilson B.  This does not mean there is an
error, it is simply a reflection of the Wilson B's insensitivity to
atoms with large B.

   I do not believe comparing the average B to the Wilson B has any
utility at all.

Dale Tronrud

On 3/12/2019 11:34 AM, Eze Chivi wrote:
> Dear CCP4bb community,
> 
> 
> The average B-factor (calculated from model) of my protein is 65,
> whereas the Wilson B is 52. I have read in this BB that "it is expected
> that average B does not deviate strongly from the Wilson B". How I can
> evaluate if the difference calculated for my data is razonable or not?
> 
> 
> Thank you in advance
> 
> 
> Ezequiel
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 



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[ccp4bb] acceptable difference between Average B-factor and Wilson B

[Eze Chivi]

Dear CCP4bb community,


The average B-factor (calculated from model) of my protein is 65, whereas the 
Wilson B is 52. I have read in this BB that "it is expected that average B does 
not deviate strongly from the Wilson B". How I can evaluate if the difference 
calculated for my data is razonable or not?


Thank you in advance


Ezequiel



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Re: [ccp4bb] Protein modeling issue

[Raymond Brown]

Yes you are absolutely right. I believe the problem is the difficulty of 
fitting valine, leucine and isoleucine rotomers and sidechains to what are 
essentially "blobs" of map density. Refinement has a hard time with this.
I guess we have to stick with the experimental density.

Best

Ray

On Sun, 3/10/19, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> 
wrote:

 Subject: Re: [ccp4bb] Protein modeling issue
 To: CCP4BB@JISCMAIL.AC.UK
 Date: Sunday, March 10, 2019, 3:40 PM
 
 Both
 REFMAC and COOT have an option to regularise (coot) or
 idealise (refmac) a structure. These options will correct
 bad gemetry if possible, but pay no attention to the fit to
 density.
 In general i think
 it is sensible to inspect the map for regions where there
 are serious errors high lighted. However if the resolution
 is low, or the region of the protein is poorly ordered, it
 may be difficult to see what needs fixing.
 Eleanor
 On Sat, 9 Mar 2019
 at 21:23, Raymond Brown 
 wrote:
 Hi
 folks,
 
 
 
 The WHATIF server found the following issue in evaluating a
 protein structure.
 
 
 
 Structure Z-scores, positive is better than average:
 
 
 
 chi-1 / chi-2 rotamer normality  :  -7.278       
  (bad             (  -3.8,  1.6) )
 
 
 
 
 
 RMS Z-scores, should be close to 1.0:
 
 
 
 Improper dihedral distribution :     2.025       
  (loose)
 
 
 
 
 
 Does anyone have a suggestion of what can be done for
 example 
 
 in Coot or Refmac5 to improve or fix these results?
 
 
 
 
 
 Many thanks
 
 Ray Brown
 
 
 
 
 
 
 
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 link:
 
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 the following link:
 
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[ccp4bb] Faculty positions in cryoEM at King's College London

[Steiner, Roberto]

Dear Colleagues

I would like to draw your attention on the following Lecturer/Senior Lecturer 
positions in cryoEM available at King’s College London. Closing date for the 
application is 11-Apr-2019.

https://my.corehr.com/pls/kingrecruit/erq_jobspec_version_4.display_form?p_company=1_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=011466

https://my.corehr.com/pls/kingrecruit/erq_jobspec_version_4.display_form?p_company=1_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=011489

With best wishes

Professor Roberto Steiner
Randall Centre of Cell and Molecular Biophysics
Faculty of Life Sciences and Medicine
King's College London

roberto.stei...@kcl.ac.uk
Phone 0044 20 78488216
Fax0044 20 78486435

Room 3.10A
New Hunt's House
Guy's Campus
SE1 1UL
London









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Re: [ccp4bb] Refmac5 refinement question

[Robbie Joosten]

Hi Ray,

Not necessarily close to 1.00 but rather 1.00 or lower.

Cheers,
Robbie

-Original Message-
From: Raymond Brown [mailto:ray-br...@att.net] 
Sent: Tuesday, March 12, 2019 15:56
To: Robbie Joosten
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac5 refinement question

Hi Robbie,

Thank you for your very clear explanation and suggestions. 

Am I right in thinking that what this means is that the zBOND and zANGLE values 
in Refmac5 refinement should be made to be close to 1.000?

Best

Ray






On Tue, 3/12/19, Robbie Joosten  wrote:

 Subject: Re: [ccp4bb] Refmac5 refinement question
 To: CCP4BB@JISCMAIL.AC.UK
 Date: Tuesday, March 12, 2019, 4:58 AM
 
 Hi Ray,
 
 This is how I see it: Because different bond
 length and angle target tolerances/sigmas you cannot compare
 them on an absolute scale. What is less likely? A two 0.020A
 deviation in the CD1-CG in PHE or a the same deviation in
 the CD1-CG bond in LEU. If you think they are equally
 likely, you can use rmsd, if not you probably realise that
 you are comparing apples and oranges. 
 Enter
 rmsZ. Instead of comparing the absolute deviations you
 compare the deviations expressed in sigma (the Z-score).
 This brings everything on the same scale so you can actually
 compare them (provided the restraints themselves, especially
 the sigmas, make sense). 
 Now let's
 assume that your deviations (expressed as Z-scores) have a
 normal distribution. Then the rmsZ says something about the
 broadness of this distribution. With rmsZ equal to 1 your
 distribution is as wide as that of the source of the
 restraints (i.e. small molecule structures in the COD, in
 the case of Refmac). Assuming that your data are a bit
 worse, you can argue that you do not have any strong
 evidence to allow wider distributions. That means your rmsZ
 should not be greater than 1. There seems to be a bit of a
 downward trend with resolution and rmsZ: lower resolution,
 lower rmsZ. However the correlation is not very strong and
 therefor I would say that any rmsZ < 1.00 is fine. Refmac
 gives these numbers for bond lengths and angles, not for
 chiral volumes, but those all have the same sigma
 (AFAIK).
 
 Don't go for
 hard numbers with deviations, unless you find a good
 rationale to do so (if you do, please share it). I've
 seen too many case of grossly over/underrestrained models
 where a much better fit to the data (and other validation
 criteria) can be obtained by just playing a bit with the
 geometric restraint weights. 
 
 HTH,
 Robbie
   
 
 
 -Original
 Message-
 From: CCP4 bulletin board
 [mailto:CCP4BB@JISCMAIL.AC.UK]
 On Behalf Of Raymond Brown
 Sent: Monday,
 March 11, 2019 17:11
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Refmac5 refinement
 question
 
 Hi folks,
 
 What are acceptable values for
 RMS Bond length, RMS Bond angle and RMS Chiral volume?
 
 The tutorial suggests RMS Bond
 length of 0.0200?
 
 I would
 like to hear your suggestions and/or rationale.
 
 Many thanks
 
 Ray Brown
 
 
 
 To unsubscribe from the CCP4BB
 list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
 
 
 
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 list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
 



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Re: [ccp4bb] Refmac5 refinement question

[Raymond Brown]

Hi Robbie,

Thank you for your very clear explanation and suggestions. 

Am I right in thinking that what this means is that the zBOND and zANGLE values 
in Refmac5 refinement should be made to be close to 1.000?

Best

Ray






On Tue, 3/12/19, Robbie Joosten  wrote:

 Subject: Re: [ccp4bb] Refmac5 refinement question
 To: CCP4BB@JISCMAIL.AC.UK
 Date: Tuesday, March 12, 2019, 4:58 AM
 
 Hi Ray,
 
 This is how I see it: Because different bond
 length and angle target tolerances/sigmas you cannot compare
 them on an absolute scale. What is less likely? A two 0.020A
 deviation in the CD1-CG in PHE or a the same deviation in
 the CD1-CG bond in LEU. If you think they are equally
 likely, you can use rmsd, if not you probably realise that
 you are comparing apples and oranges. 
 Enter
 rmsZ. Instead of comparing the absolute deviations you
 compare the deviations expressed in sigma (the Z-score).
 This brings everything on the same scale so you can actually
 compare them (provided the restraints themselves, especially
 the sigmas, make sense). 
 Now let's
 assume that your deviations (expressed as Z-scores) have a
 normal distribution. Then the rmsZ says something about the
 broadness of this distribution. With rmsZ equal to 1 your
 distribution is as wide as that of the source of the
 restraints (i.e. small molecule structures in the COD, in
 the case of Refmac). Assuming that your data are a bit
 worse, you can argue that you do not have any strong
 evidence to allow wider distributions. That means your rmsZ
 should not be greater than 1. There seems to be a bit of a
 downward trend with resolution and rmsZ: lower resolution,
 lower rmsZ. However the correlation is not very strong and
 therefor I would say that any rmsZ < 1.00 is fine. Refmac
 gives these numbers for bond lengths and angles, not for
 chiral volumes, but those all have the same sigma
 (AFAIK).
 
 Don't go for
 hard numbers with deviations, unless you find a good
 rationale to do so (if you do, please share it). I've
 seen too many case of grossly over/underrestrained models
 where a much better fit to the data (and other validation
 criteria) can be obtained by just playing a bit with the
 geometric restraint weights. 
 
 HTH,
 Robbie
   
 
 
 -Original
 Message-
 From: CCP4 bulletin board
 [mailto:CCP4BB@JISCMAIL.AC.UK]
 On Behalf Of Raymond Brown
 Sent: Monday,
 March 11, 2019 17:11
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Refmac5 refinement
 question
 
 Hi folks,
 
 What are acceptable values for
 RMS Bond length, RMS Bond angle and RMS Chiral volume?
 
 The tutorial suggests RMS Bond
 length of 0.0200?
 
 I would
 like to hear your suggestions and/or rationale.
 
 Many thanks
 
 Ray Brown
 
 
 
 To unsubscribe from the CCP4BB
 list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
 
 
 
 To unsubscribe from the CCP4BB
 list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
 



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[ccp4bb] FEBS advanced/practical course "Biomolecules in Action II", Hamburg, June 23-28, 2019

[mesters]

Save the date:*June 23-28, 2019, Hamburg*, Germany

*FEBS Advanced Course: Biomolecules in Action II. 
*Lectures and practical 
exercises with focus on the latest, most applicable, and emerging 
bioanalytical methods applied in life sciences in order to characterize 
biomolecules for later studies involving novel radiation sources such as 
free electron lasers and complementary techniques e.g. CryoEM.


Target audience: PhD students and young postdoctoral fellows (30 places 
available)


Venue: DESY and EuXFEL

Homepage:https://biomolaction2019.febsevents.org

Poster:https://biomolaction2019.febsevents.org/download/PC19-044_Poster.pdf

Course organizers: Christian Betzel (Hamburg University) and Jeroen 
Mesters (Lübeck University)






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Re: [ccp4bb] 3D

[Philippe BENAS]

Dear all,

I do agree with Paul: VR is just perspective images that don't give you a 
stereoscopic view and is hence poorer.

This being said it is possible to build a structure in mono:  all you need is 
to have enough and the right projections in the plane...

I started 20 years ago using side by side stereo and as long as my eyes will be 
ok I could always get back at least to this option but it would be a real shame 
to loose hardware stereo...

All the best,
Philippe


Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
15, rue René Descartes
F-67084 STRASBOURG cedex
+33.3.8841.7109

E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:   http://www-ibmc.u-strasbg.fr/ , http://www-ibmc.u-strasbg.fr/spip-arn/





En date de : Lun 11.3.19, Paul Emsley  a écrit :

 Objet: Re: [ccp4bb] 3D
 À: CCP4BB@JISCMAIL.AC.UK
 Date: Lundi 11 mars 2019, 20h22
 
 On 11/03/19 15:55, Pedro Matias
 wrote:
 >
 > Reading the
 news piece, I would hardly consider the present-day VR
 > headsets to be "affordable" -
 except perhaps for the PSVR. With the
 >
 added downside that they are single-user.
 >
 > When can we expect a
 CootVR release ?
 >
 >
 
 VR is not
 really a substitute for stereo I feel (or vice versa).
 
 CootVR is available from
 github: it's in "beta" at the moment
 
 https://github.com/hamishtodd1/CVR
 
 The author of CootVR is Hamish
 Todd. There is a release planned for May
 (2019).
 
 Regards,
 
 Paul
 
 
 
 To unsubscribe from the CCP4BB
 list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
 



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Re: [ccp4bb] Refmac5 refinement question

[Robbie Joosten]

Hi Ray,

This is how I see it: Because different bond length and angle target 
tolerances/sigmas you cannot compare them on an absolute scale. What is less 
likely? A two 0.020A deviation in the CD1-CG in PHE or a the same deviation in 
the CD1-CG bond in LEU. If you think they are equally likely, you can use rmsd, 
if not you probably realise that you are comparing apples and oranges. 
Enter rmsZ. Instead of comparing the absolute deviations you compare the 
deviations expressed in sigma (the Z-score). This brings everything on the same 
scale so you can actually compare them (provided the restraints themselves, 
especially the sigmas, make sense). 
Now let's assume that your deviations (expressed as Z-scores) have a normal 
distribution. Then the rmsZ says something about the broadness of this 
distribution. With rmsZ equal to 1 your distribution is as wide as that of the 
source of the restraints (i.e. small molecule structures in the COD, in the 
case of Refmac). Assuming that your data are a bit worse, you can argue that 
you do not have any strong evidence to allow wider distributions. That means 
your rmsZ should not be greater than 1. There seems to be a bit of a downward 
trend with resolution and rmsZ: lower resolution, lower rmsZ. However the 
correlation is not very strong and therefor I would say that any rmsZ < 1.00 is 
fine. Refmac gives these numbers for bond lengths and angles, not for chiral 
volumes, but those all have the same sigma (AFAIK).

Don't go for hard numbers with deviations, unless you find a good rationale to 
do so (if you do, please share it). I've seen too many case of grossly 
over/underrestrained models where a much better fit to the data (and other 
validation criteria) can be obtained by just playing a bit with the geometric 
restraint weights. 

HTH,
Robbie
   

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raymond 
Brown
Sent: Monday, March 11, 2019 17:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refmac5 refinement question

Hi folks,

What are acceptable values for RMS Bond length, RMS Bond angle and RMS Chiral 
volume?

The tutorial suggests RMS Bond length of 0.0200?

I would like to hear your suggestions and/or rationale.

Many thanks

Ray Brown



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[ccp4bb] Multiple Postdoctoral Fellowships available at the “Multiscale Research Institute for Complex Systems” at Fudan University of Shanghai

[lyguo]

Dear all,
The Multiscale Research Institute for Complex Systems (MRICS) at Fudan 
University is located at the Zhangjiang Campus of Fudan University and is 
supported by the Shanghai High-peak Program. MRICS is strongly committed to the 
development of noveland effective multi-scale imaging technology that spans 
microscopic molecular structures all the way to macroscopic medical imaging, 
with the aim to provide unprecedented spatial and temporal insights into the 
structures and functions of living beings at all levels (molecules, cells, 
tissues, organs and even whole organisms).MRICS isequipped witha 
state-of-the-art cryo-EM facility that includesFEI Titan Krios equipped with 
Volta phase plate, Glacios, Talos and Aquilos. It is also located next to 
Shanghai Synchrotron Radiation Facility for X-ray crystallography.
Our team includes Nobel laureate and international leading interdisciplinary 
experts.
We are now open to recruit a number of postdoctoral fellows with trainingsin 
various scientific fields. These include but are not limited to:
1.Structural biology(X-ray crystallography and cryo-electron microscopy
including single-particle and tomography);
2.Biochemistry or protein chemistry(no structural biology background is
required);
3.Genetics, epigenetics or cell biology(experience in cell or tissue
imaging is preferred);
4.Computational biology(the development of large-scale molecular dynamics
simulation algorithms, algorithmic development related to electron microscopy
imaging techniques, and the application of artificial intelligence in biology.
We particularly welcome applicants with Ph.D. degree in theoretical physics,
computational physics or condensed matter physics);
5.Development of experimental animal disease models(experience inexperimental 
animal research is preferred).


Other criteria:
1) Recent Ph.D. graduates
(within three years of graduation) from a well-known university or research 
institute anywhere in theworld;
2) Fluent in English;
3) Published high-level research articles in the past three years.

Compensation:
1) We offer internationally competitive annual salary, the level will be 
determined according to the applicant's experience and qualification;
2) We will assist in applying for low-rent housing in Shanghai and provide 
certain housing subsidies;
3) We have ample opportunities to collaborate with renown laboratories 
worldwide;
4) We provide support for applying for funding opportunities whenever 
applicable.


For interested applicants,please submit postdoctoral application packages 
including resumes, conciseresearch interest statements, representative 
publications, phone numbers and email addresses of three academic referees 
to:Miss Lingyue Guo (Email:ly...@fudan.edu.cn).
We look forward to your joining of our first-class team!



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