Re: [COOT] CHO H-bonds.

[Ian Tickle]

Hi Jan

Thanks for the suggestion.  I checked & AFAICS the wavelength is correct.
I think in any case the difference you are talking about would be far too
small to explain the effect I'm seeing (the error in the wavelength is ~
0.01% whereas I'm seeing deviations from the ideal vdW contact of up to
15%!).

My conclusion is that this is not due to any kind of error, it is a real
effect.  CH...O bonds are well-documented (thanks to Patrick Loll and Scott
Horowitz for useful references), even though it appears that MP (and PDB
validation) takes absolutely no account of them!

Cheers

-- Ian


On 2 July 2015 at 08:27, Jan Stransky  wrote:

>  About the unit cell shrinkage:
>
> I have heard a lecture (I believe it was Andrea Thorn form G. Sheldrick
> group on one of CCP4 meetings), where she mentioned a mistake in X-ray
> wavelenght input (swaped 3rd and 4th digit), which no program from
> integration to structure solution did not recognised. It appeared in
> structure refinement in wrong bond distances.
>
> Worth of checking.
>
> Jan
>
>
> On 07/01/2015 10:58 AM, Ian Tickle wrote:
>
>
>  Paul, as an aside to this, would it be possible to have it so that if the
> relevant boxes in the "Environment Distances" menu are checked then H-bonds
> and.or bumps are automatically re-calculated on re-centering?  Currently
> it's necessary to check off & on one of the boxes every time the view is
> re-centered.  If I forget to do that it's very easy to miss bumps (and I
> don't have a great deal of faith in MP's concept of what constitutes a
> bump)!
>
>  Cheers
>
>  -- Ian
>
>
> On 30 June 2015 at 14:33, Ian Tickle  wrote:
>
>>
>>  Hello All
>>
>>  I guess this is really a question about MolProbity (and possibly about
>> autoBuster) but I assume that most Coot users will be using the MolProbity
>> validation tools.
>>
>>  I am in the process of depositing 4 structures of the same protein
>> (different ligands) and I noticed that MP seems to be reporting an
>> unusually large number of bumps in both the "small overlap" and "bad
>> overlap" classes.  In each case the resolution is 2 Ang., the structures
>> have been refined by autoBuster and the density seems to be unequivocal,
>> see e.g.:
>>
>>
>> https://drive.google.com/file/d/0B4H4H-DyO60-SEQwS1k5S3RIVG8/view?usp=sharing
>>
>>  A lot of the bumps are main-chain CHalpha to main-chain carbonyl O
>> H-bonds, but there are also some CH...O side-chain H-bonds, again with
>> clear density.  The C...O distances are in the range 3.0 to 3.2 Ang., so
>> too short for a vdW contact.  The H...O distances are ~ 2.2 Ang. which is
>> definitely shorter than the sum of the vdW radii ( H: 1.2 + O: 1.5 = 2.7).
>>
>>  I found this survey of CH...O H-bonds but it's restricted to CH...O
>> bonds at the end of helices and I see them mostly in sheets.
>>
>> http://www.mrc-lmb.cam.ac.uk/genomes/madanm/pdfs/chapter1.pdf
>>
>>  This reports 11 examples (i.e. H-bonds, not structures) in the 3.0-3.2
>> range for the whole of the PDB (admittedly as it was in 2001 when the
>> article appears to have been written).  I have about the same number in one
>> structure!
>>
>>  One possibility I considered was that the unit cells had all somehow
>> 'shrunk'.  This can be tested with WhatCheck: however it only reports a
>> very small shrinkage which translates to an error of ~ 0.02 Ang. in a 3
>> Ang. distance, which is nowhere near enough to explain a discrepancy of 0.5
>> Ang.
>>
>>  So I guess my question is has anyone else noticed this in their MP
>> dot-plots; also does anyone know what criteria does MP uses for testing
>> bumps and specifically what value is it using for CH...O H-bonds?  And of
>> course I'd like to know whether this will affect my percentile ranking in
>> the clashscore from the PDB validation!
>>
>>  Cheers
>>
>>  -- Ian
>>
>>
>
> --
> Jan Stransky, PhD student
> Institute of Biotechnology, CAS
> Laboratory of structure and function of biomolecules
> Nad Safinou II 366
> Vestec
> Czech Republic
>
> Tel.: +420226201570
>
>

Re: [COOT] CHO H-bonds.

[Jan Stransky]

Dear Tim,
I know that it cause rescaling and you don't have to input the number 
manually most of the time recently. I just wanted to point out that it 
can obviously happend. The question reminded me Andrea's lecture.

Jan

On 07/02/2015 10:34 AM, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jan,

when you input the wrong wavelength during data processing, you
rescale the Ewald sphere construction, i.e. it will result in a
different unit cell and crystal to detector distance.

I am not sure what you mean by 'which no program from
integration to structure solution did not recognised'. How should the
downstream software detect the human mistake?
The wavelength you enter should of course be double checked.

Nowadays this seldomly occurs because the experimental settings are
usually transferred automatically and reliably between the beamline
software and the processing tools.

Cheers,
Tim

On 07/02/2015 09:27 AM, Jan Stransky wrote:

About the unit cell shrinkage:

I have heard a lecture (I believe it was Andrea Thorn form G.
Sheldrick group on one of CCP4 meetings), where she mentioned a
mistake in X-ray wavelenght input (swaped 3rd and 4th digit), which
no program from integration to structure solution did not
recognised. It appeared in structure refinement in wrong bond
distances.

Worth of checking.

Jan

On 07/01/2015 10:58 AM, Ian Tickle wrote:

Paul, as an aside to this, would it be possible to have it so
that if the relevant boxes in the "Environment Distances" menu
are checked then H-bonds and.or bumps are automatically
re-calculated on re-centering?  Currently it's necessary to check
off & on one of the boxes every time the view is re-centered.  If
I forget to do that it's very easy to miss bumps (and I don't
have a great deal of faith in MP's concept of what constitutes a
bump)!

Cheers

-- Ian


On 30 June 2015 at 14:33, Ian Tickle mailto:ianj...@gmail.com>> wrote:


Hello All

I guess this is really a question about MolProbity (and possibly
about autoBuster) but I assume that most Coot users will be
using the MolProbity validation tools.

I am in the process of depositing 4 structures of the same
protein (different ligands) and I noticed that MP seems to be
reporting an unusually large number of bumps in both the "small
overlap" and "bad overlap" classes.  In each case the resolution
is 2 Ang., the structures have been refined by autoBuster and the
density seems to be unequivocal, see e.g.:


https://drive.google.com/file/d/0B4H4H-DyO60-SEQwS1k5S3RIVG8/view?usp=sharing





A lot of the bumps are main-chain CHalpha to main-chain carbonyl O

H-bonds, but there are also some CH...O side-chain H-bonds,
again with clear density.  The C...O distances are in the range
3.0 to 3.2 Ang., so too short for a vdW contact. The H...O
distances are ~ 2.2 Ang. which is definitely shorter than the sum
of the vdW radii ( H: 1.2 + O: 1.5 = 2.7).

I found this survey of CH...O H-bonds but it's restricted to
CH...O bonds at the end of helices and I see them mostly in
sheets.

http://www.mrc-lmb.cam.ac.uk/genomes/madanm/pdfs/chapter1.pdf

This reports 11 examples (i.e. H-bonds, not structures) in the
3.0-3.2 range for the whole of the PDB (admittedly as it was in
2001 when the article appears to have been written).  I have
about the same number in one structure!

One possibility I considered was that the unit cells had all
somehow 'shrunk'. This can be tested with WhatCheck: however it
only reports a very small shrinkage which translates to an error
of ~ 0.02 Ang. in a 3 Ang. distance, which is nowhere near
enough to explain a discrepancy of 0.5 Ang.

So I guess my question is has anyone else noticed this in their
MP dot-plots; also does anyone know what criteria does MP uses
for testing bumps and specifically what value is it using for
CH...O H-bonds?  And of course I'd like to know whether this will
affect my percentile ranking in the clashscore from the PDB
validation!

Cheers

-- Ian


- -- 
- --

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149

GPG Key ID = A46BEE1A

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Version: GnuPG v1

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--
Jan Stransky, PhD student
Institute of Biotechnology, CAS
Laboratory of structure and function of biomolecules
Nad Safinou II 366
Vestec
Czech Republic

Tel.: +420226201570

Re: [COOT] CHO H-bonds.

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jan,

when you input the wrong wavelength during data processing, you
rescale the Ewald sphere construction, i.e. it will result in a
different unit cell and crystal to detector distance.

I am not sure what you mean by 'which no program from
integration to structure solution did not recognised'. How should the
downstream software detect the human mistake?
The wavelength you enter should of course be double checked.

Nowadays this seldomly occurs because the experimental settings are
usually transferred automatically and reliably between the beamline
software and the processing tools.

Cheers,
Tim

On 07/02/2015 09:27 AM, Jan Stransky wrote:
> About the unit cell shrinkage:
> 
> I have heard a lecture (I believe it was Andrea Thorn form G.
> Sheldrick group on one of CCP4 meetings), where she mentioned a
> mistake in X-ray wavelenght input (swaped 3rd and 4th digit), which
> no program from integration to structure solution did not
> recognised. It appeared in structure refinement in wrong bond
> distances.
> 
> Worth of checking.
> 
> Jan
> 
> On 07/01/2015 10:58 AM, Ian Tickle wrote:
>> 
>> Paul, as an aside to this, would it be possible to have it so
>> that if the relevant boxes in the "Environment Distances" menu
>> are checked then H-bonds and.or bumps are automatically
>> re-calculated on re-centering?  Currently it's necessary to check
>> off & on one of the boxes every time the view is re-centered.  If
>> I forget to do that it's very easy to miss bumps (and I don't
>> have a great deal of faith in MP's concept of what constitutes a
>> bump)!
>> 
>> Cheers
>> 
>> -- Ian
>> 
>> 
>> On 30 June 2015 at 14:33, Ian Tickle > > wrote:
>> 
>> 
>> Hello All
>> 
>> I guess this is really a question about MolProbity (and possibly 
>> about autoBuster) but I assume that most Coot users will be
>> using the MolProbity validation tools.
>> 
>> I am in the process of depositing 4 structures of the same
>> protein (different ligands) and I noticed that MP seems to be
>> reporting an unusually large number of bumps in both the "small
>> overlap" and "bad overlap" classes.  In each case the resolution
>> is 2 Ang., the structures have been refined by autoBuster and the
>> density seems to be unequivocal, see e.g.:
>> 
>> 
>> https://drive.google.com/file/d/0B4H4H-DyO60-SEQwS1k5S3RIVG8/view?usp=sharing
>>
>>
>>
>> 
A lot of the bumps are main-chain CHalpha to main-chain carbonyl O
>> H-bonds, but there are also some CH...O side-chain H-bonds,
>> again with clear density.  The C...O distances are in the range
>> 3.0 to 3.2 Ang., so too short for a vdW contact. The H...O
>> distances are ~ 2.2 Ang. which is definitely shorter than the sum
>> of the vdW radii ( H: 1.2 + O: 1.5 = 2.7).
>> 
>> I found this survey of CH...O H-bonds but it's restricted to 
>> CH...O bonds at the end of helices and I see them mostly in
>> sheets.
>> 
>> http://www.mrc-lmb.cam.ac.uk/genomes/madanm/pdfs/chapter1.pdf
>> 
>> This reports 11 examples (i.e. H-bonds, not structures) in the 
>> 3.0-3.2 range for the whole of the PDB (admittedly as it was in 
>> 2001 when the article appears to have been written).  I have
>> about the same number in one structure!
>> 
>> One possibility I considered was that the unit cells had all 
>> somehow 'shrunk'. This can be tested with WhatCheck: however it 
>> only reports a very small shrinkage which translates to an error 
>> of ~ 0.02 Ang. in a 3 Ang. distance, which is nowhere near
>> enough to explain a discrepancy of 0.5 Ang.
>> 
>> So I guess my question is has anyone else noticed this in their
>> MP dot-plots; also does anyone know what criteria does MP uses
>> for testing bumps and specifically what value is it using for
>> CH...O H-bonds?  And of course I'd like to know whether this will
>> affect my percentile ranking in the clashscore from the PDB
>> validation!
>> 
>> Cheers
>> 
>> -- Ian
>> 
>> 
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149

GPG Key ID = A46BEE1A

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=V1FJ
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Re: [COOT] CHO H-bonds.

[Jan Stransky]

About the unit cell shrinkage:

I have heard a lecture (I believe it was Andrea Thorn form G. Sheldrick 
group on one of CCP4 meetings), where she mentioned a mistake in X-ray 
wavelenght input (swaped 3rd and 4th digit), which no program from 
integration to structure solution did not recognised. It appeared in 
structure refinement in wrong bond distances.


Worth of checking.

Jan

On 07/01/2015 10:58 AM, Ian Tickle wrote:


Paul, as an aside to this, would it be possible to have it so that if 
the relevant boxes in the "Environment Distances" menu are checked 
then H-bonds and.or bumps are automatically re-calculated on 
re-centering?  Currently it's necessary to check off & on one of the 
boxes every time the view is re-centered.  If I forget to do that it's 
very easy to miss bumps (and I don't have a great deal of faith in 
MP's concept of what constitutes a bump)!


Cheers

-- Ian


On 30 June 2015 at 14:33, Ian Tickle > wrote:



Hello All

I guess this is really a question about MolProbity (and possibly
about autoBuster) but I assume that most Coot users will be using
the MolProbity validation tools.

I am in the process of depositing 4 structures of the same protein
(different ligands) and I noticed that MP seems to be reporting an
unusually large number of bumps in both the "small overlap" and
"bad overlap" classes.  In each case the resolution is 2 Ang., the
structures have been refined by autoBuster and the density seems
to be unequivocal, see e.g.:


https://drive.google.com/file/d/0B4H4H-DyO60-SEQwS1k5S3RIVG8/view?usp=sharing

A lot of the bumps are main-chain CHalpha to main-chain carbonyl O
H-bonds, but there are also some CH...O side-chain H-bonds, again
with clear density.  The C...O distances are in the range 3.0 to
3.2 Ang., so too short for a vdW contact. The H...O distances are
~ 2.2 Ang. which is definitely shorter than the sum of the vdW
radii ( H: 1.2 + O: 1.5 = 2.7).

I found this survey of CH...O H-bonds but it's restricted to
CH...O bonds at the end of helices and I see them mostly in sheets.

http://www.mrc-lmb.cam.ac.uk/genomes/madanm/pdfs/chapter1.pdf

This reports 11 examples (i.e. H-bonds, not structures) in the
3.0-3.2 range for the whole of the PDB (admittedly as it was in
2001 when the article appears to have been written).  I have about
the same number in one structure!

One possibility I considered was that the unit cells had all
somehow 'shrunk'. This can be tested with WhatCheck: however it
only reports a very small shrinkage which translates to an error
of ~ 0.02 Ang. in a 3 Ang. distance, which is nowhere near enough
to explain a discrepancy of 0.5 Ang.

So I guess my question is has anyone else noticed this in their MP
dot-plots; also does anyone know what criteria does MP uses for
testing bumps and specifically what value is it using for CH...O
H-bonds?  And of course I'd like to know whether this will affect
my percentile ranking in the clashscore from the PDB validation!

Cheers

-- Ian




--
Jan Stransky, PhD student
Institute of Biotechnology, CAS
Laboratory of structure and function of biomolecules
Nad Safinou II 366
Vestec
Czech Republic

Tel.: +420226201570

Re: [COOT] CHO H-bonds.

[Ian Tickle]

Paul, as an aside to this, would it be possible to have it so that if the
relevant boxes in the "Environment Distances" menu are checked then H-bonds
and.or bumps are automatically re-calculated on re-centering?  Currently
it's necessary to check off & on one of the boxes every time the view is
re-centered.  If I forget to do that it's very easy to miss bumps (and I
don't have a great deal of faith in MP's concept of what constitutes a
bump)!

Cheers

-- Ian


On 30 June 2015 at 14:33, Ian Tickle  wrote:

>
> Hello All
>
> I guess this is really a question about MolProbity (and possibly about
> autoBuster) but I assume that most Coot users will be using the MolProbity
> validation tools.
>
> I am in the process of depositing 4 structures of the same protein
> (different ligands) and I noticed that MP seems to be reporting an
> unusually large number of bumps in both the "small overlap" and "bad
> overlap" classes.  In each case the resolution is 2 Ang., the structures
> have been refined by autoBuster and the density seems to be unequivocal,
> see e.g.:
>
>
> https://drive.google.com/file/d/0B4H4H-DyO60-SEQwS1k5S3RIVG8/view?usp=sharing
>
> A lot of the bumps are main-chain CHalpha to main-chain carbonyl O
> H-bonds, but there are also some CH...O side-chain H-bonds, again with
> clear density.  The C...O distances are in the range 3.0 to 3.2 Ang., so
> too short for a vdW contact.  The H...O distances are ~ 2.2 Ang. which is
> definitely shorter than the sum of the vdW radii ( H: 1.2 + O: 1.5 = 2.7).
>
> I found this survey of CH...O H-bonds but it's restricted to CH...O bonds
> at the end of helices and I see them mostly in sheets.
>
> http://www.mrc-lmb.cam.ac.uk/genomes/madanm/pdfs/chapter1.pdf
>
> This reports 11 examples (i.e. H-bonds, not structures) in the 3.0-3.2
> range for the whole of the PDB (admittedly as it was in 2001 when the
> article appears to have been written).  I have about the same number in one
> structure!
>
> One possibility I considered was that the unit cells had all somehow
> 'shrunk'.  This can be tested with WhatCheck: however it only reports a
> very small shrinkage which translates to an error of ~ 0.02 Ang. in a 3
> Ang. distance, which is nowhere near enough to explain a discrepancy of 0.5
> Ang.
>
> So I guess my question is has anyone else noticed this in their MP
> dot-plots; also does anyone know what criteria does MP uses for testing
> bumps and specifically what value is it using for CH...O H-bonds?  And of
> course I'd like to know whether this will affect my percentile ranking in
> the clashscore from the PDB validation!
>
> Cheers
>
> -- Ian
>
>