RMS angles and comprehensive validation in phenix

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C

18 Sep 2014 18 Sep '14

8:32 p.m.

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Pavel Afonine

19 Sep 19 Sep

6:57 a.m.

Hi, if you make sure these values are not caused by a handful of atoms that flew a distance apart for whatever reason then values like ok to me. This is why looking at a histogram of deviations (bond, angles etc) is way more useful than looking at just one number! Pavel On 9/18/14 1:32 PM, C wrote:

...

Hi,

Refining using phenix I find the RMS angle drifting towards 2.3-2.7 range when validating the resulting structure.

These are high resolution structures and I was wondering if someone could comment on whether 2.3-2.7 values are worrisome? Thank you

Katherine Sippel

4:50 p.m.

This is from Phenix's FAQ page... *"My resolution is X Angstroms; what should RMS(bonds) and RMS(angles) be?* This is somewhat controversial, but absolute upper limits for a well-refined protein structure at high resolution are typically 0.02 for RMS(bonds) and 2.0 for RMS(angles); usually they will be significantly lower. As resolution decreases the acceptable deviation from geometry restraints also decreases, so at 3.5 Angstrom, more appropriate values would be 0.01 and 1.0." If the histogram shows that the RMS(angles) average higher than 2 then I think that would be a result of poorly refined structures skewing the graph rather than a reflection of what the RMS should be. On Fri, Sep 19, 2014 at 1:57 AM, Pavel Afonine wrote:

...

Hi,

if you make sure these values are not caused by a handful of atoms that flew a distance apart for whatever reason then values like ok to me. This is why looking at a histogram of deviations (bond, angles etc) is way more useful than looking at just one number!

Pavel

On 9/18/14 1:32 PM, C wrote:

Hi,

Refining using phenix I find the RMS angle drifting towards 2.3-2.7 range when validating the resulting structure.

These are high resolution structures and I was wondering if someone could comment on whether 2.3-2.7 values are worrisome? Thank you

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- "Nil illegitimo carborundum"* - *Didactylos

George Devaniranjan

5:38 p.m.

If the RMS of angles are so deviant and the structure is high resolution then wouldn't it show up in COOT density fitting? On Fri, Sep 19, 2014 at 12:50 PM, Katherine Sippel < [email protected]> wrote:

...

This is from Phenix's FAQ page...

*"My resolution is X Angstroms; what should RMS(bonds) and RMS(angles) be?*

This is somewhat controversial, but absolute upper limits for a well-refined protein structure at high resolution are typically 0.02 for RMS(bonds) and 2.0 for RMS(angles); usually they will be significantly lower. As resolution decreases the acceptable deviation from geometry restraints also decreases, so at 3.5 Angstrom, more appropriate values would be 0.01 and 1.0."

If the histogram shows that the RMS(angles) average higher than 2 then I think that would be a result of poorly refined structures skewing the graph rather than a reflection of what the RMS should be.

On Fri, Sep 19, 2014 at 1:57 AM, Pavel Afonine wrote:

...
Hi,

if you make sure these values are not caused by a handful of atoms that flew a distance apart for whatever reason then values like ok to me. This is why looking at a histogram of deviations (bond, angles etc) is way more useful than looking at just one number!

Pavel

On 9/18/14 1:32 PM, C wrote:

Hi,

Refining using phenix I find the RMS angle drifting towards 2.3-2.7 range when validating the resulting structure.

These are high resolution structures and I was wondering if someone could comment on whether 2.3-2.7 values are worrisome? Thank you

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- "Nil illegitimo carborundum"* - *Didactylos

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Edward A. Berry

6:05 p.m.

Two different histograms involved here? For one structure, histogram of the deviations at all the different bonds, angles For the entire PDB, histogram of rmsd of all the different structures On 09/19/2014 12:50 PM, Katherine Sippel wrote:

...

This is from Phenix's FAQ page...

*"My resolution is X Angstroms; what should RMS(bonds) and RMS(angles) be?*

This is somewhat controversial, but absolute upper limits for a well-refined protein structure at high resolution are typically 0.02 for RMS(bonds) and 2.0 for RMS(angles); usually they will be significantly lower. As resolution decreases the acceptable deviation from geometry restraints also decreases, so at 3.5 Angstrom, more appropriate values would be 0.01 and 1.0."

If the histogram shows that the RMS(angles) average higher than 2 then I think that would be a result of poorly refined structures skewing the graph rather than a reflection of what the RMS should be.

On Fri, Sep 19, 2014 at 1:57 AM, Pavel Afonine mailto:[email protected]> wrote:

Hi,

if you make sure these values are not caused by a handful of atoms that flew a distance apart for whatever reason then values like ok to me. This is why looking at a histogram of deviations (bond, angles etc) is way more useful than looking at just one number!

Pavel

On 9/18/14 1:32 PM, C wrote:

...
Hi,

Refining using phenix I find the RMS angle drifting towards 2.3-2.7 range when validating the resulting structure.

These are high resolution structures and I was wondering if someone could comment on whether 2.3-2.7 values are worrisome? Thank you

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- "Nil illegitimo carborundum"/- /Didactylos

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Pavel Afonine

6:21 p.m.

Hi Ed, yes, that's right. One is to detect severe outliers that may screw up the overall numbers. The other one is to compare these overall numbers with those derived from similar structures available in the data base. Pavel On 9/19/14 11:05 AM, Edward A. Berry wrote:

...

Two different histograms involved here? For one structure, histogram of the deviations at all the different bonds, angles For the entire PDB, histogram of rmsd of all the different structures

On 09/19/2014 12:50 PM, Katherine Sippel wrote:

...
This is from Phenix's FAQ page...

*"My resolution is X Angstroms; what should RMS(bonds) and RMS(angles) be?*

This is somewhat controversial, but absolute upper limits for a well-refined protein structure at high resolution are typically 0.02 for RMS(bonds) and 2.0 for RMS(angles); usually they will be significantly lower. As resolution decreases the acceptable deviation from geometry restraints also decreases, so at 3.5 Angstrom, more appropriate values would be 0.01 and 1.0."

If the histogram shows that the RMS(angles) average higher than 2 then I think that would be a result of poorly refined structures skewing the graph rather than a reflection of what the RMS should be.

On Fri, Sep 19, 2014 at 1:57 AM, Pavel Afonine mailto:[email protected]> wrote:

Hi,

if you make sure these values are not caused by a handful of atoms that flew a distance apart for whatever reason then values like ok to me. This is why looking at a histogram of deviations (bond, angles etc) is way more useful than looking at just one number!

Pavel

On 9/18/14 1:32 PM, C wrote:

...
Hi,

Refining using phenix I find the RMS angle drifting towards 2.3-2.7 range when validating the resulting structure.

These are high resolution structures and I was wondering if someone could comment on whether 2.3-2.7 values are worrisome? Thank you

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- "Nil illegitimo carborundum"/- /Didactylos

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Katherine Sippel

6:38 p.m.

The point I was trying to make was that, assuming that there are no large outliers skewing the final RMS(angles), an overall RMS of 2.3-2.7 would be worrisome. On Fri, Sep 19, 2014 at 1:21 PM, Pavel Afonine wrote:

...

Hi Ed,

yes, that's right. One is to detect severe outliers that may screw up the overall numbers. The other one is to compare these overall numbers with those derived from similar structures available in the data base.

Pavel

On 9/19/14 11:05 AM, Edward A. Berry wrote:

...
Two different histograms involved here? For one structure, histogram of the deviations at all the different bonds, angles For the entire PDB, histogram of rmsd of all the different structures

On 09/19/2014 12:50 PM, Katherine Sippel wrote:

...
This is from Phenix's FAQ page...

*"My resolution is X Angstroms; what should RMS(bonds) and RMS(angles) be?*

This is somewhat controversial, but absolute upper limits for a well-refined protein structure at high resolution are typically 0.02 for RMS(bonds) and 2.0 for RMS(angles); usually they will be significantly lower. As resolution decreases the acceptable deviation from geometry restraints also decreases, so at 3.5 Angstrom, more appropriate values would be 0.01 and 1.0."

If the histogram shows that the RMS(angles) average higher than 2 then I think that would be a result of poorly refined structures skewing the graph rather than a reflection of what the RMS should be.

On Fri, Sep 19, 2014 at 1:57 AM, Pavel Afonine mailto:[email protected]> wrote:

Hi,

if you make sure these values are not caused by a handful of atoms that flew a distance apart for whatever reason then values like ok to me. This is why looking at a histogram of deviations (bond, angles etc) is way more useful than looking at just one number!

Pavel

On 9/18/14 1:32 PM, C wrote:

...
Hi,

Refining using phenix I find the RMS angle drifting towards 2.3-2.7 range when validating the resulting structure.

These are high resolution structures and I was wondering if someone could comment on whether 2.3-2.7 values are worrisome? Thank you

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- "Nil illegitimo carborundum"/- /Didactylos

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- "Nil illegitimo carborundum"* - *Didactylos

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C
Edward A. Berry
George Devaniranjan
Katherine Sippel
Pavel Afonine