CCP4 Bulletin Board Archive: Optimisation of weights

From: ‪<kavya

Date: 14 October 2011 06:12

Dear users,

Can the optimization of the X-ray weighing factor

and B-factor (overall wt) as mentioned in the paper

Acta Cryst. (2007). D63, 1274–1281 by Dr.Ian Tickel,

be used for the refinement of the data sets beyond

the resolution range mentioned in the paper: 1.33 -

2.55 Ang?

Also the structures that were used to optimize these

parameters were already solved and refined, so when

we are solving a new structure to what extent does the

model has to be built before starting the optimization?

Thanking you

With Regards

M. Kavyashree

----------

From: Ian Tickle

Hi Kavya

The resolutions of the structures mentioned in the paper were only

examples, the Rfree/-LLfree minimisation method (which are actually

due to Axel Brunger & Gerard Bricogne respectively) does not depend on

resolution.

If the structures are already solved & refined, you don't need to do

any model building, it should be within the radius of convergence with

the new weights - it's only a small adjustment after all.

Cheers

-- Ian

----------

From: ‪<kavya‬

Date: 14 October 2011 11:19

Respected Sir,

For one of the structures that I did optimisation

had values - (resolution of the data - 2.35Ang)

Before optimization- (Bfactor weight=1.0, X-ray Weight - auto)

R factor 0.2362

R free 0.2924

-LLfree 7521.8

rmsBOND 0.0160

zBOND 0.660

After optimisation- (B-factor weight=0.2, X-ray Weight - 0.08)

R factor 0.2327

R free 0.2882

-LLfree 7495.7

rmsBOND 0.0111

zBOND 0.460

Also can you tell me what is the limit for B-factor weight hat can be varied.

Sorry I just re-read your last email and realised and didn't read it

properly the first time. But what I said still stands: you can of

course try to optimise the weights at an early stage (before adding

waters say), there's no harm doing that, but there's also not much

point since you'll have to do it all again with the complete model,

since adding a lot of waters will undoubtedly change the optimal

weights. So I just leave the weight optimisation until the model is

complete. As long as the initial weights are "in the same ball park",

so that your RMSZ(bonds) is around 0.5 for typical resolutions (a bit

lower for low resolution, a bit higher for very high resolution) it

won't affect interpretation of maps etc.

Cheers

-- Ian

On Fri, Oct 14, 2011 at 9:37 AM, Ian Tickle wrote:

> It must be the same complete model that you refined previously, I

> doubt that it will give the correct answer if you leave out the waters

> for example.

> You say "there was quite a difference". Could you be more specific:

> what were the values of the weights, R factors and RMSZ(bonds/angles)

> before and after weight optimisation?

> Cheers

> -- Ian

----------

From: Ian Tickle

Hi your X-ray weight of .08 seems very small, the optimal value is

normally in the range 1 to 4 (I usually set it initially at the

median, i.e. 2.5). But which weight keyword did you use "WEIGHT

MATRIX .08" or "WEIGHT AUTO .08" (the latter is I think undocumented,

so I'm guessing the first)? Anyway I would strongly advise the

latter: the difference is that the MATRIX weight is on a completely

arbitrary scale, whereas the AUTO weight is at least relative to the

theoretical value of 1 (even though the optimal value may not be 1 in

practice, at least your initial guess will be in the same ball park).

Note that what Refmac calls "automatic weighting" is not the same as

what X-PLOR, CNS & phenix call "automatic weighting" (at least that's

my understanding). "WEIGHT AUTO" in Refmac is the same as "WEIGHT

AUTO 10", whereas auto-weighting in X-PLOR corresponds to "WEIGHT AUTO

1" in Refmac. Not surprisingly these give quite different results!

The optimal B factor weight is also around 1, see the paper for typical values.

I'm still not clear precisely what you meant by ""there was quite a

difference". I don't see that big a difference between the 2 runs,

just a slight tightening up of the geometry. Are you saying you see

big differences in the refined co-ordinates? That would be a cause

for concern.

Cheers

-- Ian

From: ‪<kavya‬

Date: 14 October 2011 12:01

Respected Sir,

Yes, the weight mentioned in the paper was

weight matrix, but the one i used was the

option under "Refinement parameters- weighing

term (when auto weighing is turned off)".

But If I really wasnt to change the weight matrix

where should I change (in the code?)?

No, I dint mean a big difference, not in the

coordinates, but the values of R-factors and

other terms. I thought it was quite different.

So you mean that it is not of much concern?

Thanking you

With Regards

M. Kavyashree

----------

From: Ian Tickle

Date: 14 October 2011 12:03

No, the weights referred to in the paper are definitely the ones given

as "WEIGHT AUTO x". I can say that with confidence because I never

use "WEIGHT MATRIX x" for reasons I explained. I think what I said is

that it's _related_ to the matrix weight, which it obviously is by

some constant but unknown factor.

You don't have to change any code (that has been done for you!), but

if you're using CCP4I (sorry I don't so I can't give you precise

instructions), you probably have to edit the script before submission

(there should be a button in the "Run" menu for that).

Cheers

-- Ian

I would say that it's not a big difference, just tightening up of the

geometry, as I said.

Cheers

-- Ian

From: ‪<kavya

Date: 14 October 2011 08:42

Respected Sir,

Thank you for your clarification. I had adopted this

method recently. My doubt was if we have to optimize

these two parameters during refinement, should we have

the whole model along with water and ligands or only

protein with few water positioning is enough. The reason

why I am asking because there was quite a difference

when I refined the same structure without the optimization

and with optimization of these two parameters.

Thanking you

With regards

M. Kavyashree

From: Ian Tickle

Sent by: CCP4 bulletin board

Date: 10/14/2011 12:34PM

Subject: Re: [ccp4bb] Optimisation of weights

Hi Kavya

The resolutions of the structures mentioned in the paper were only

examples, the Rfree/-LLfree minimisation method (which are actually

due to Axel Brunger & Gerard Bricogne respectively) does not depend on

resolution.

If the structures are already solved & refined, you don't need to do

any model building, it should be within the radius of convergence with

the new weights - it's only a small adjustment after all.

Cheers

-- Ian

On Fri, Oct 14, 2011 at 6:12 AM, <kavya@ssl.serc.iisc.ernet.in> wrote:

> Dear users,

> Can the optimization of the X-ray weighing factor

> and B-factor (overall wt) as mentioned in the paper

> Acta Cryst. (2007). D63, 1274–1281 by Dr.Ian Tickel,

> be used for the refinement of the data sets beyond

> the resolution range mentioned in the paper: 1.33 -

> 2.55 Ang?

> Also the structures that were used to optimize these

> parameters were already solved and refined, so when

> we are solving a new structure to what extent does the

> model has to be built before starting the optimization?

> Thanking you

> With Regards

> M. Kavyashree

> --

> This message has been scanned for viruses and

> dangerous content by MailScanner, and is

> believed to be clean.

----------

From: Ian Ticklek

It must be the same complete model that you refined previously, I

doubt that it will give the correct answer if you leave out the waters

for example.

You say "there was quite a difference". Could you be more specific:

what were the values of the weights, R factors and RMSZ(bonds/angles)

before and after weight optimisation?