Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

[sonali dhindwal]

Dear All,

I want to thank all for your helpful and quick suggestions and insight.

It was a very good discussion and also helped in understanding the topic.

Thanks again.

-- 
Sonali Dhindwal

“Live as if you were to die tomorrow. Learn as if you were to live forever.”

--- On Mon, 18/3/13, Ian Tickle  wrote:

From: Ian Tickle 
Subject: Re: [ccp4bb] Query regarding the use of anisotropic temperature factor 
and ideal rmsAngle and rmsBond length values
To: CCP4BB@JISCMAIL.AC.UK
Date: Monday, 18 March, 2013, 4:06 AM

On 17 March 2013 13:19, Robbie Joosten  wrote:






Small 
addition to Ian's comment. The value you give with 'weight auto $value' 
is a starting value. Refmac will gradually change it if needed (it's 
autoweighting after all) and your starting value
 does matter somewhat. Based on Ian's advice PDB_REDO uses a starting 
value of 2.50 which seems to do the trick most of the times.



Cheers,

Robbie

Good point, here's an example from a Refmac log file of that 
happening in practice using Refmac_5.8.0031 (output redacted so not 
showing every iteration):


  Data line--- WEIGHT AUTO 0.95

 Weight matrix   1.00564407E-02
 Actual weight   0.9499  is applied to the X-ray term
 
 Weight matrix   1.19658876E-02
 Actual weight   0.9499  is applied to the X-ray term



 Weight matrix   1.67442132E-02
 Actual weight    1.234  is applied to the X-ray term

 Weight matrix   2.25313306E-02
 Actual weight    1.6054999  is applied to the X-ray term

 Weight matrix   2.31216233E-02


 Actual weight    1.6054999  is applied to the X-ray term
 
 Weight matrix   2.32296251E-02
 Actual weight    1.6054999  is applied to the X-ray term

 Weight matrix   2.34125387E-02
 Actual weight    1.6054999  is applied to the X-ray term



 Weight matrix   3.04648653E-02
 Actual weight    2.0871499  is applied to the X-ray term

 Weight matrix   3.05170882E-02
 Actual weight    2.0871499  is applied to the X-ray term



So here I inputted Wa = 0.95 (I deliberately chose it too small), and 
Refmac calculates what the equivalent value of Wm (1.00564407E-02) would
 have been (i.e. inputting WEIGHT MATRIX 1.00564407E-02 would have given
 identical results to WEIGHT AUTO 0.95).  However what is actually used 
('Actual weight') in the refinement calculation is Wa.  Then Wa is 
automatically optimised according to Refmac's internal criteria, giving a
 final optimised value Wa = 2.09.  Note that Wm changes as the model is 
improved even when Wa is kept fixed.

 
Cheers

-- Ian

[ccp4bb] Build DNA to fit density

[Wei Shi]

Hi all,
I am refining a structure of protein-DNA complex with coot. The DNA in
my search model is shorter than the DNA in the crystal, and now I
could see the density for extra DNA(6 base pairs) on either end of the
search model DNA. But, I don't know how to build the extra DNA back to
fit the density or whether I should build the whole DNA manually to
fit the density.
I used calculate-> other model tools-> ideal DNA/RNA to generate a 6
base pairs (B form) and then, I use calculate->
model/fit/refine->rotate/Translate molecule to move the 6 bp long
stretch of double strand DNA to fit the density, but it's hard for me
to fit the DNA into the density and it seems that the B form DNA I
generate doesn't
fit the density well. I am wondering how to fit the DNA into the
density and whether we could fit the DNA into density like we add
amino acid to fit the density.
Thank you so much!

Best,
Wei

[ccp4bb] Off topic: Oligonucleotide purity

[Theresa Hsu]

Dear all

What is the right (cost wise) purity level for DNA oligonucleotide synthesized 
for cloning, site-directed mutagenesis and protein/DNA co-crystallisation?

Thank you.

Theresa

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

[Ian Tickle]

On 17 March 2013 13:19, Robbie Joosten  wrote:
Small addition to Ian's comment. The value you give with 'weight auto
$value' is a starting value. Refmac will gradually change it if needed
(it's autoweighting after all) and your starting value does matter
somewhat. Based on Ian's advice PDB_REDO uses a starting value of 2.50
which seems to do the trick most of the times.

Cheers,
Robbie

Good point, here's an example from a Refmac log file of that happening in
practice using Refmac_5.8.0031 (output redacted so not showing every
iteration):

  Data line--- WEIGHT AUTO 0.95

 Weight matrix   1.00564407E-02
 Actual weight   0.9499  is applied to the X-ray term

 Weight matrix   1.19658876E-02
 Actual weight   0.9499  is applied to the X-ray term

 Weight matrix   1.67442132E-02
 Actual weight1.234  is applied to the X-ray term

 Weight matrix   2.25313306E-02
 Actual weight1.6054999  is applied to the X-ray term

 Weight matrix   2.31216233E-02
 Actual weight1.6054999  is applied to the X-ray term

 Weight matrix   2.32296251E-02
 Actual weight1.6054999  is applied to the X-ray term

 Weight matrix   2.34125387E-02
 Actual weight1.6054999  is applied to the X-ray term

 Weight matrix   3.04648653E-02
 Actual weight2.0871499  is applied to the X-ray term

 Weight matrix   3.05170882E-02
 Actual weight2.0871499  is applied to the X-ray term

So here I inputted Wa = 0.95 (I deliberately chose it too small), and
Refmac calculates what the equivalent value of Wm (1.00564407E-02) would
have been (i.e. inputting WEIGHT MATRIX 1.00564407E-02 would have given
identical results to WEIGHT AUTO 0.95).  However what is actually used
('Actual weight') in the refinement calculation is Wa.  Then Wa is
automatically optimised according to Refmac's internal criteria, giving a
final optimised value Wa = 2.09.  Note that Wm changes as the model is
improved even when Wa is kept fixed.

Cheers

-- Ian



>

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

[Ethan Merritt]

On Sunday, 17 March 2013, Pavel Afonine wrote:
> Hi Ethan,
> 
> 
> I would place the expected resolution break-even point at more like
> > 1.2 - 1.3 A.  But that's only an expectation, not a rule to rely on.
> > You should justify anisotropic refinement of a structure on the basis
> > of its own particular model and measured data.  Robbie Joosten has
> > already pointed out that you can use the PDB-Redo scripts to test
> > whether individual anisotropic ADPs are justified.
> >
> 
> when it comes to a point when a choice of refinement strategy cannot be
> uniquely and reliably chosen based on theoretical considerations, that
> opens a great opportunity for endless perennial discussions like this. My
> point was that if you are lucky and there isn't many options (in this case
> there are only two: iso vs aniso!) there is an easier, quicker and robust
> alternative: simply try both and that will give your THE answer. Perhaps
> not very scientific (no monster formula derived) but quick, easy and robust!
> 
> 
> > > - higher than 1.2A: all anisotropic (macromolelcule, water, ligands)
> > > - lower than 1.7A: all isotropic;
> > > - 1.5-1.7A is a grey area where there is only one single way to know for
> > > sure: try both (isotropic and anisotropic) and see which one works best.
> > > I realize "works best" is a broad term, but I would say Rwork, Rfree,
> > > Rfree-Rwork and values of refined anisotropic ADPs should be enough to
> > make
> > > a decision.
> >
> > Unfortunately, Rfree cannot be used reliably for this purpose.
> >
> 
> Yes, Rfree cannot be used for this purpose reliably, very true. This is
> exactly why I wrote above ".. Rwork, Rfree, Rfree-Rwork *and values of
> refined anisotropic ADPs* should be enough to make a decision." My
> understanding is that your "To B.." method is one of possible ways of
> looking at the values of refined anisotropic B-factors.

That is a misunderstanding that misses the fundamental point.
Looking at the refined ADPs only helps in the artificial case that
you have a known-correct set of ADPs as a point of comparison for the 
newly refined ADPS [*].

You cannot do that in the case of a new structure.
  
The Hamilton R test does not look at the individual ADPs or at any other
refined parameter values.  It looks only at the crystallographic residuals
and the respective degrees of freedom.  In this sense it is analagous
to comparing Rfree values, but as demonstrated in the paper the Hamilton
test can correctly detect an invalid model in cases where Rfree cannot.

Ethan


[*] Of course if the new ADPs are inherently unreasonable, for instance
non-positive definite, that is good reason to reject the model.
But I am assuming that a properly behaving refinement program will not
produce such an inherently unbelievable model.  Instead the outcome
of refinement will be internally consistent, plausible, but wrong.
You won't learn that just by inspecting the ADPs it produces.


> All the best,
> Pavel
> 

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

[Pavel Afonine]

Hi Ethan,


I would place the expected resolution break-even point at more like
> 1.2 - 1.3 A.  But that's only an expectation, not a rule to rely on.
> You should justify anisotropic refinement of a structure on the basis
> of its own particular model and measured data.  Robbie Joosten has
> already pointed out that you can use the PDB-Redo scripts to test
> whether individual anisotropic ADPs are justified.
>

when it comes to a point when a choice of refinement strategy cannot be
uniquely and reliably chosen based on theoretical considerations, that
opens a great opportunity for endless perennial discussions like this. My
point was that if you are lucky and there isn't many options (in this case
there are only two: iso vs aniso!) there is an easier, quicker and robust
alternative: simply try both and that will give your THE answer. Perhaps
not very scientific (no monster formula derived) but quick, easy and robust!


> > - higher than 1.2A: all anisotropic (macromolelcule, water, ligands)
> > - lower than 1.7A: all isotropic;
> > - 1.5-1.7A is a grey area where there is only one single way to know for
> > sure: try both (isotropic and anisotropic) and see which one works best.
> > I realize "works best" is a broad term, but I would say Rwork, Rfree,
> > Rfree-Rwork and values of refined anisotropic ADPs should be enough to
> make
> > a decision.
>
> Unfortunately, Rfree cannot be used reliably for this purpose.
>

Yes, Rfree cannot be used for this purpose reliably, very true. This is
exactly why I wrote above ".. Rwork, Rfree, Rfree-Rwork *and values of
refined anisotropic ADPs* should be enough to make a decision." My
understanding is that your "To B.." method is one of possible ways of
looking at the values of refined anisotropic B-factors.

All the best,
Pavel

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

[Ethan Merritt]

On Sunday, 17 March 2013, Pavel Afonine wrote:
> Hi Sonali,
> 
> regarding isotropic vs anisotropic parameterization of your individual
> ADPs: apart from common sense and theoretical considerations, this is also
> in great part software dependent.
> 
> I can't speak for other programs, but for phenix.refine I would say the
> rule of thumb is:
> - higher than 1.5A: refine macromolecule with individual anisotropic ADPs
> (the rest - isotropic);

I would place the expected resolution break-even point at more like
1.2 - 1.3 A.  But that's only an expectation, not a rule to rely on.
You should justify anisotropic refinement of a structure on the basis
of its own particular model and measured data.  Robbie Joosten has
already pointed out that you can use the PDB-Redo scripts to test
whether individual anisotropic ADPs are justified.

> - higher than 1.2A: all anisotropic (macromolelcule, water, ligands)
> - lower than 1.7A: all isotropic;
> - 1.5-1.7A is a grey area where there is only one single way to know for
> sure: try both (isotropic and anisotropic) and see which one works best.
> I realize "works best" is a broad term, but I would say Rwork, Rfree,
> Rfree-Rwork and values of refined anisotropic ADPs should be enough to make
> a decision.

Unfortunately, Rfree cannot be used reliably for this purpose.  

Please see my "To B or not to B" Acta D paper from last year
for worked examples of why Rfree cannot be trusted in this case.
In particular, in the 1.5 - 1.7A region Rfree is likely to
indicate incorrectly that anisotropic refinement is OK, whereas
"peeking at the answer sheet" (i.e. using a known structure where
true atomic resolution data is available) demonstrates that the
anisotropic refinement is garbage even though Rfree is improved.

cheers,

Ethan

> If it's not a neutron data, H atoms should be always isotropic (kind of
> obvious, but mentioning it just in case..).
> 
> Good luck,
> Pavel
> 
> On Sun, Mar 17, 2013 at 1:06 AM, sonali dhindwal <
> sonali11dhind...@yahoo.co.in> wrote:
> 
> > Dear All,
> >
> > We want little suggestion and knowledge regarding refinement of data in
> > Refmac. We have a data with resolution upto 1.5A. Overall redundancy of 5.5
> > and 3.7 in high resolution bin. and I over Sigma is also 21 overall and
> > 2.2 in last resolution bin.
> >
> > When we first did isotropic refinement we used automatic weighing term,
> > which gave good Rfree and Rfactor of 18.4 and 16.9 but high rmsBond and
> > rmsAngle of 0.027 and 2.5 respectively. We were able to improve rmsBond and
> > rmsAngle values by decreasing weighing term to 0.5.
> >
> > But when we do anisotropic refinement with weighing term of 0.5 it gives
> > Rfree, Rfactor and FOM of 16.8, 15.0 and 90.7 respectively. And rmsAngle
> > and rmsBond of 0.0074 and 1.25.
> >
> > Now, we want to know what should be the ideal values for rmsAngle and
> > rmsBond at such resolution. Secondly, if we can use anisotropic refinement
> > with such data.
> >
> > All your suggestions will be highly valuable.
> > Thanks in advance.
> >
> > --
> > Sonali Dhindwal
> >
> > “Live as if you were to die tomorrow. Learn as if you were to live
> > forever.”
> >
> 

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

[Pavel Afonine]

Hi Sonali,

regarding isotropic vs anisotropic parameterization of your individual
ADPs: apart from common sense and theoretical considerations, this is also
in great part software dependent.

I can't speak for other programs, but for phenix.refine I would say the
rule of thumb is:
- higher than 1.5A: refine macromolecule with individual anisotropic ADPs
(the rest - isotropic);
- higher than 1.2A: all anisotropic (macromolelcule, water, ligands)
- lower than 1.7A: all isotropic;
- 1.5-1.7A is a grey area where there is only one single way to know for
sure: try both (isotropic and anisotropic) and see which one works best.
I realize "works best" is a broad term, but I would say Rwork, Rfree,
Rfree-Rwork and values of refined anisotropic ADPs should be enough to make
a decision.

If it's not a neutron data, H atoms should be always isotropic (kind of
obvious, but mentioning it just in case..).

Good luck,
Pavel

On Sun, Mar 17, 2013 at 1:06 AM, sonali dhindwal <
sonali11dhind...@yahoo.co.in> wrote:

> Dear All,
>
> We want little suggestion and knowledge regarding refinement of data in
> Refmac. We have a data with resolution upto 1.5A. Overall redundancy of 5.5
> and 3.7 in high resolution bin. and I over Sigma is also 21 overall and
> 2.2 in last resolution bin.
>
> When we first did isotropic refinement we used automatic weighing term,
> which gave good Rfree and Rfactor of 18.4 and 16.9 but high rmsBond and
> rmsAngle of 0.027 and 2.5 respectively. We were able to improve rmsBond and
> rmsAngle values by decreasing weighing term to 0.5.
>
> But when we do anisotropic refinement with weighing term of 0.5 it gives
> Rfree, Rfactor and FOM of 16.8, 15.0 and 90.7 respectively. And rmsAngle
> and rmsBond of 0.0074 and 1.25.
>
> Now, we want to know what should be the ideal values for rmsAngle and
> rmsBond at such resolution. Secondly, if we can use anisotropic refinement
> with such data.
>
> All your suggestions will be highly valuable.
> Thanks in advance.
>
> --
> Sonali Dhindwal
>
> “Live as if you were to die tomorrow. Learn as if you were to live
> forever.”
>

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

[Jrh]

Dear Dr Zhu,
I hope the following might make things easier to grasp. The 3.0Angstrom 
diffraction resolution is basically required to resolve a protein polypeptide 
chain whether your protein is in an 80% solvent content unit cell or a 50% 
solvent content unit cell. You will have more observations in the former than 
in the latter to reach that goal. In the days of a single counter four circle 
diffractometer that was a major overhead. As has been alluded to in 
considerable detail in other replies solvent flattening does however give phase 
determination benefits and 80% is better than 50%.
Yours sincerely,
John

Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 15 Mar 2013, at 00:27, Guangyu Zhu  wrote:

> I have this question. For exmaple, a protein could be crystallized in two 
> crystal forms. Two crystal form have same space group, and 1 molecule/asymm. 
> One crystal form diffracts to 3A with 50% solvent; and the other diffracts to 
> 3.6A with 80% solvent. The cell volume of 3.6A crystal must be 5/2=2.5 times 
> larger because of higher solvent content. If both data collecte to same 
> completeness (say 100%), 3.6A data actually have higher data/parameter ratio, 
> 5/2/(3.6/3)**3= 1.45 times to 3A data. For refinement, better data/parameter 
> should give more accurate structure, ie. 3.6A data is better. But higher 
> resolution should give a better resolved electron density map. So which 
> crystal form really give a better (more reliable and accurate) protein 
> structure?

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

[Colin Nave]

One issue is whether the extra data for the 80% solvent volume consists of 
independent measurements. The references below suggest that the required  
"oversampling " of intensities is given when one has a 50% solvent volume.

J. Miao, D. Sayre, and H. N. Chapman, "Phase retrieval from the magnitude of 
the Fourier transforms of nonperiodic objects," J. Opt. Soc. Am. A 15, 
1662-1669 (1998)
Or
Q. 
Shen,
 I. 
Bazarov
 and P. 
Thibault
 Diffractive imaging of nonperiodic materials with future coherent X-ray 
sources J. Synchrotron Rad. (2004). 11, 432-438

Of course the above assumes everything is ideal.

Colin

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Guangyu 
Zhu
Sent: 15 March 2013 00:28
To: ccp4bb
Subject: [ccp4bb] Resolution and data/parameter ratio, which one is more 
important?

I have this question. For exmaple, a protein could be crystallized in two 
crystal forms. Two crystal form have same space group, and 1 molecule/asymm. 
One crystal form diffracts to 3A with 50% solvent; and the other diffracts to 
3.6A with 80% solvent. The cell volume of 3.6A crystal must be 5/2=2.5 times 
larger because of higher solvent content. If both data collecte to same 
completeness (say 100%), 3.6A data actually have higher data/parameter ratio, 
5/2/(3.6/3)**3= 1.45 times to 3A data. For refinement, better data/parameter 
should give more accurate structure, ie. 3.6A data is better. But higher 
resolution should give a better resolved electron density map. So which crystal 
form really give a better (more reliable and accurate) protein structure?



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Re: [ccp4bb] Please remove my email from the list shodawade...@gmail.com

[Santosh]

Hello,
I have been using this portal for past eight years, learned many intricate
aspects of crystallography. now that I have changed my career please make
sure to remove me from the list.
I wish you all wonderful years and best wishes.
Sincerely,
Santosh

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

[Robbie Joosten]

Small addition to Ian's comment. The value you give with 'weight auto $value' 
is a starting value. Refmac will gradually change it if needed (it's 
autoweighting after all) and your starting value does matter somewhat. Based on 
Ian's advice PDB_REDO uses a starting value of 2.50 which seems to do the trick 
most of the times.

Cheers,
Robbie

Sent from my Windows Phone

From: Ian Tickle
Sent: 2013-03-17 13:15
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Query regarding the use of anisotropic temperature factor 
and ideal rmsAngle and rmsBond length values

Hi Sonali

The 'WEIGHT MATRIX Wm' scale factor, to which I assume you're referring, is
on a relative, not absolute, scale so is not comparable between different
models, i.e. the results will be substantially different when you change
the model keeping Wm fixed as you discovered.  If you want the weight to be
more easily comparable for different models (and also for data with
different resolution limits) you need it to be on an absolute scale: this
is what you get with 'WEIGHT AUTO Wa'.  For a theoretically perfect model
the optimal value of Wa would be 1, i.e. the geometrical and X-ray weights
would be on the same absolute scale, though in practice the optimal value
of Wa usually turns out to be a little higher than 1 (say between 1 and
4).  The default Wa value (using just 'WEIGHT AUTO') is 10: I find this is
suitable for refining MR solutions where you need the model to be less
geometrically rigid so the X-ray contribution needs to be inflated
relatively, but as the model improves Wa needs to be decreased towards the
theoretical value of 1 (or certainly not much less than 1).

Note that this Wa is conveniently the same as the Wa used in X-PLOR, CNS &
phenix.refine (so it can be transferred between programs), though in the
latter case I believe it stands for weight(absolute), not
weight(automatic).  If I have this wrong, no doubt the
X-PLOR/CNS/phenix.refine people will put me straight!

Other than that I agree with everything Robbie said & you should heed his
advice.

Cheers

-- Ian


On 17 March 2013 08:06, sonali dhindwal wrote:

> Dear All,
>
> We want little suggestion and knowledge regarding refinement of data in
> Refmac. We have a data with resolution upto 1.5A. Overall redundancy of 5.5
> and 3.7 in high resolution bin. and I over Sigma is also 21 overall and
> 2.2 in last resolution bin.
>
> When we first did isotropic refinement we used automatic weighing term,
> which gave good Rfree and Rfactor of 18.4 and 16.9 but high rmsBond and
> rmsAngle of 0.027 and 2.5 respectively. We were able to improve rmsBond and
> rmsAngle values by decreasing weighing term to 0.5.
>
> But when we do anisotropic refinement with weighing term of 0.5 it gives
> Rfree, Rfactor and FOM of 16.8, 15.0 and 90.7 respectively. And rmsAngle
> and rmsBond of 0.0074 and 1.25.
>
> Now, we want to know what should be the ideal values for rmsAngle and
> rmsBond at such resolution. Secondly, if we can use anisotropic refinement
> with such data.
>
> All your suggestions will be highly valuable.
> Thanks in advance.
>
> --
> Sonali Dhindwal
>
> “Live as if you were to die tomorrow. Learn as if you were to live
> forever.”
>

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

[Ian Tickle]

Hi Sonali

The 'WEIGHT MATRIX Wm' scale factor, to which I assume you're referring, is
on a relative, not absolute, scale so is not comparable between different
models, i.e. the results will be substantially different when you change
the model keeping Wm fixed as you discovered.  If you want the weight to be
more easily comparable for different models (and also for data with
different resolution limits) you need it to be on an absolute scale: this
is what you get with 'WEIGHT AUTO Wa'.  For a theoretically perfect model
the optimal value of Wa would be 1, i.e. the geometrical and X-ray weights
would be on the same absolute scale, though in practice the optimal value
of Wa usually turns out to be a little higher than 1 (say between 1 and
4).  The default Wa value (using just 'WEIGHT AUTO') is 10: I find this is
suitable for refining MR solutions where you need the model to be less
geometrically rigid so the X-ray contribution needs to be inflated
relatively, but as the model improves Wa needs to be decreased towards the
theoretical value of 1 (or certainly not much less than 1).

Note that this Wa is conveniently the same as the Wa used in X-PLOR, CNS &
phenix.refine (so it can be transferred between programs), though in the
latter case I believe it stands for weight(absolute), not
weight(automatic).  If I have this wrong, no doubt the
X-PLOR/CNS/phenix.refine people will put me straight!

Other than that I agree with everything Robbie said & you should heed his
advice.

Cheers

-- Ian


On 17 March 2013 08:06, sonali dhindwal wrote:

> Dear All,
>
> We want little suggestion and knowledge regarding refinement of data in
> Refmac. We have a data with resolution upto 1.5A. Overall redundancy of 5.5
> and 3.7 in high resolution bin. and I over Sigma is also 21 overall and
> 2.2 in last resolution bin.
>
> When we first did isotropic refinement we used automatic weighing term,
> which gave good Rfree and Rfactor of 18.4 and 16.9 but high rmsBond and
> rmsAngle of 0.027 and 2.5 respectively. We were able to improve rmsBond and
> rmsAngle values by decreasing weighing term to 0.5.
>
> But when we do anisotropic refinement with weighing term of 0.5 it gives
> Rfree, Rfactor and FOM of 16.8, 15.0 and 90.7 respectively. And rmsAngle
> and rmsBond of 0.0074 and 1.25.
>
> Now, we want to know what should be the ideal values for rmsAngle and
> rmsBond at such resolution. Secondly, if we can use anisotropic refinement
> with such data.
>
> All your suggestions will be highly valuable.
> Thanks in advance.
>
> --
> Sonali Dhindwal
>
> “Live as if you were to die tomorrow. Learn as if you were to live
> forever.”
>

Re: [ccp4bb] qtrview command line options

[vellieux]

Wonderful, thanks very much to all the CCP4 team !

[ I have met users who object to "command lines" and "terminals" and 
"no-clicking", for them if it's not in the GUI it's "yuk" but I guess 
that you can't have everything :-) ]


Fred.

On 16/03/13 22:16, andrey.lebe...@stfc.ac.uk wrote:

After ccp4 update No 19, Log–files can be opened with qtrview from the command 
line:

logview name.log

This also works for log-files generated with "quick scale" and "quick symmetry" 
from imosflm.

If ccp4 database entries do not exist, input and output files will not be shown 
in the viewer
(except for "quick scale" and "quick symmetry" files).

Regards

Andrey



On 11 Mar 2013, at 20:06, Lebedev, Andrey (STFC,RAL,SC) wrote:


Hi Ed

Thank you for the suggestion.
We are looking into this and hopefully will provide a solution soon.

Regards

Andrey


On 11 Mar 2013, at 14:26, Ed Pozharski wrote:


Is there some way of opening a log file (specifically, the
pointandscale.log that imosflm bridge to scala generates) with qtrview
from command line?

I tried, of course, this

qtrview pointandscale.log

but it opens empty, no log-file. I tried qtrview -h and qtrview --help
and man qtrview but there is seemingly no documentation.

I found the source code (yes, I can google) and can deduce that
available options at startup are

--log-file
--report-xml
--report-xrt
--inp-file

The only thing that works is

qrtview --log-file pointandscale.log

but that only shows me the log-file itself, i.e. no graphs etc.  I
understand that the program was designed primarily for ccp4 gui and I
know loggraph (and it works).

By the way, checkout instructions for the qtrview repository at

https://fg.oisin.rc-harwell.ac.uk/projects/qtrview/

don't work throwing this error

bzr: ERROR: Connection error: curl connection error (server certificate
verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile:
none)
on https://fg.oisin.rc-harwell.ac.uk/anonscm/bzr/qtrview/.bzr/smart

Cheers,

Ed.

--
"Hurry up before we all come back to our senses!"
  Julian, King of Lemurs



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

[Robbie Joosten]

Dear Sonali,

There is no such thing as an ideal rmsd for bonds and angles given resolution. 
IMO you should use rmsZ which also doesn't have an ideal value. If its below 1 
your good. As for the isotropic vs anisotropic, you can use a hamilton test if 
you do two refinements changing only the B-factor model. Ethan Merritt had a 
paper about that last year in Acta D.

Now for the self plug: PDB_REDO automatically selects the B-factor model based 
on this test (and some more selectors) and will also optimize your weights to 
get proper rmsZ values for geometry.

Cheers,
Robbie

Sent from my Windows Phone

From: sonali dhindwal
Sent: 2013-03-17 09:06
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Query regarding the use of anisotropic temperature factor and 
ideal rmsAngle and rmsBond length values

Dear All,

We want little suggestion and knowledge regarding refinement of data in Refmac. 
We have a data with resolution upto 1.5A. Overall redundancy of 5.5 and 3.7 in 
high resolution bin. and I over Sigma is also 21 overall and  2.2 in last 
resolution bin.

When we first did isotropic refinement we used automatic weighing term, which 
gave good Rfree and Rfactor of 18.4 and 16.9 but high rmsBond and rmsAngle of 
0.027 and 2.5 respectively. We were able to improve rmsBond and rmsAngle values 
by decreasing weighing term to 0.5.

But when we do anisotropic refinement with weighing term of 0.5 it gives Rfree, 
Rfactor and FOM of 16.8, 15.0 and 90.7 respectively. And rmsAngle and rmsBond 
of 0.0074 and 1.25.

Now, we want to know what should be the ideal values for rmsAngle and rmsBond 
at such resolution. Secondly, if we can use anisotropic refinement with such 
data.

All your suggestions will be highly valuable.
Thanks in advance.

--
Sonali Dhindwal

“Live as if you were to die tomorrow. Learn as if you were to live forever.”

Re: [ccp4bb] first use of synchrotron radiation in PX

[Jrh]

Dear James,
I agree with your chronology of the first full new protein structures by SR 
MAD. 

The 1975 two wavelength Hoppe and Jakubowksi study of erythrocruorin with Ni 
and Co Kalpha Xray tubes is a classic piece of work of in effect MAD phasing . 
See the IUCr Anomalous Scattering Conference book edited by Abrahams and 
Ramaseshan.

The 1971 Nature paper biological diffraction with SR from Hamburg, whose focus 
was on muscle diffraction, which Colin highlighted, does have an entry though 
for a 'protein crystal' in a table. 

There is also of course the Hamburg 1976 paper Harmsen et al J Mol Biol but 
which generally concluded SR for protein crystallography wasn't worth it; to me 
as a doctoral student at the time this was clearly an incorrect conclusion I 
firmly believed based on the 1971 Hamburg Nature paper and especially what I 
could see in and beyond the 1976 SSRL PNAS paper.

Yours sincerely,
John

Prof John R Helliwell DSc 
 
 

On 16 Mar 2013, at 14:46, James Holton  wrote:

> The first report of shooting a protein crystal at a synchrotron (I think) was 
> in 1976:
> http://www.pnas.org/content/73/1/128.full.pdf
> that was rubredoxin
> 
> The first PDB file that contains a "SYNCHROTRON=Y" entry is 1tld (trypsin), 
> which was deposited in 1989:
> http://dx.doi.org/10.1016/0022-2836(89)90110-1
> But the structure of trypsin was arguably already "solved" at that time.

> Anomalous diffraction was first demonstrated by Coster, Knoll and Prins in 
> 1930
> http://dx.doi.org/10.1007/BF01339610
> this was 20 years before Bijvoet.  But not with a synchrotron and definitely 
> not with a protein
> 
> The first protein to be solved using anomalous was crambin in 1981:
> http://dx.doi.org/10.1038/290107a0
> but this was not using a synchrotron
> 
> The first demonstration of MAD on a protein at a synchrotron was a Tb soak of 
> parvalbumin in 1985
> http://dx.doi.org/10.1016/0014-5793(85)80207-6
> but one could argue that several parvalbumins were already known at that time.
> 
> The first MAD structure from native metals was cucumber blue copper protein 
> (2cbp) in 1989
> http://dx.doi.org/10.1126%2Fscience.3406739
> 
> The first "new" structure using MAD, as well as the first SeMet was 
> ribonuclease H (1rnh) in 1990
> http://dx.doi.org/10.1126/science.2169648
> 
> If anyone knows of earlier cases, I'd like to hear about it!
> 
> -James Holton
> MAD Scientist
> 
> On 3/13/2013 7:38 AM, Alan Cheung wrote:
>> Hi all - i'm sure this many will know this : when and what was the first 
>> protein structure solved on a synchrotron?
>> 
>> Thanks in advance
>> Alan
>> 
>> 

[ccp4bb] Query regarding the use of anisotropic temperature factor and ideal rmsAngle and rmsBond length values

[sonali dhindwal]

Dear All,

We want little suggestion and knowledge regarding refinement of data in Refmac. 
We have a data with resolution upto 1.5A. Overall redundancy of 5.5 and 3.7 in 
high resolution bin. and I over Sigma is also 21 overall and  2.2 in last 
resolution bin.

When we first did isotropic refinement we used automatic weighing term, which 
gave good Rfree and Rfactor of 18.4 and 16.9 but high rmsBond and rmsAngle of 
0.027 and 2.5 respectively. We were able to improve rmsBond and rmsAngle values 
by decreasing weighing term to 0.5.

But when we do anisotropic refinement with weighing term of 0.5 it gives Rfree, 
Rfactor and FOM of 16.8, 15.0 and 90.7 respectively. And rmsAngle and rmsBond 
of 0.0074 and 1.25.

Now, we want to know what should be the ideal values for rmsAngle and rmsBond 
at such resolution. Secondly, if we can use anisotropic refinement with such 
data.

All your suggestions will be highly valuable.
Thanks in advance.

-- 
Sonali Dhindwal

“Live as if you were to die tomorrow. Learn as if you were to live forever.”