Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

2015-02-05 Thread Alexandre OURJOUMTSEV
Hi, Bernhard,

ok, sure, you are right ! Nevertheless, I would not be so desperate and 
categorical: you are right , at my knowledge also, there is currently NO known 
algorithm to take into account the "flat mask bulk solvent contribution" at the 
rotation step (maybe I am wrong?), however this does not mean it is impossible. 
The question is should it be done at all ?
 When do you the rotation search, you need to use mostly the highest 
resolution data, and it may be rather useful to remove the low-resolution data 
(see the tests described in Acta Cryst D51, 888-895, 1995; however, it looks 
like in practice nobody uses variable resolution for different MR steps). When 
you work at low resolution with envelopes, you do not care about bulk solvent 
correction since all this results indeed in a scale coefficient.
 There is a tiny (but not unusual) situation when one wants to do MR at the 
"worse" resolution of 9-12 A (worse in the sense that the maps show neither 
(already) molecular envelope nor (yet) clear structure. Suppose we could solve 
the MR problem - what we do then since the maps are so poor ? It is worthy in 
this case artificially lower the resolution ? I do not know...

However, I agree, you question is fully valid and is interesting.


All the best ,

Sacha

De : hofkristall...@gmail.com<mailto:hofkristall...@gmail.com> 
[hofkristall...@gmail.com]
Envoyé : mercredi 4 février 2015 14:09
À : Alexandre OURJOUMTSEV; CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Objet : RE: [ccp4bb] Bulk solvent correction in Phaser MR LF
Hi Sacha,

I was imprecise. With unplaced I meant 'neither rotated nor translated'.
Once you become post-rotationally SF based, you can in fact compute a F(env)
whole inclusion should improve the TF score.

What is not evident to me is how to use a mask and compute the Fs  if the 
orientation
(rotation) is yet to be determined?

Thx, BR




Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

2015-02-04 Thread Bernhard Rupp (Hofkristallrat a.D.)
Hi Sacha,

 

I was imprecise. With unplaced I meant ‘neither rotated nor translated’. 

Once you become post-rotationally SF based, you can in fact compute a F(env)


whole inclusion should improve the TF score.

 

What is not evident to me is how to use a mask and compute the Fs  if the
orientation 

(rotation) is yet to be determined?

 

Thx, BR 

 

 

From: Alexandre OURJOUMTSEV [mailto:sa...@igbmc.fr] 
Sent: Dienstag, 3. Februar 2015 22:19
To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK
Subject: RE:[ccp4bb] Bulk solvent correction in Phaser MR LF

 

Dear Bernhard,

For the unplaced model, it can only be a Babinet model to improve the
scaling,

This is not fully true, and the flat mask correction can be used as well.
Please look :



Fokine, A. & Urzhumtsev, A.G. (2002) "On the use of low resolution data for
translation search in molecular replacement". Acta Cryst., A58, 72-74

 

Fokine, A., Capitani, G., Grütter, M.G. & Urzhumtsev, A. (2003)
"Bulk-solvent correction for fast translation search in molecular
replacement: service programs for AMoRe and CNS". J. Appl.Cryst., 36,
352-355.


Best regards,

Sacha Urzhumtsev

  _  

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Bernhard Rupp
(Hofkristallrat a.D.) [hofkristall...@gmail.com]
Envoyé : mardi 3 février 2015 14:49
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Bulk solvent correction in Phaser MR LF

Hi Fellows,

 

I cannot find the proper reference for the implementation of bulk solvent
corrections in the

Phaser Molecular replacement likelihood functions.  For the unplaced model,
it can only be a Babinet model to improve the scaling, and I believe that is
implemented via a 

Babinet rescaled function for sigma A including the coordinate error.

 

Can anybody help me where to find that?

Thx, BR

 

 



Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

2015-02-03 Thread Alexandre OURJOUMTSEV
Dear Bernhard,

For the unplaced model, it can only be a Babinet model to improve the scaling,

This is not fully true, and the flat mask correction can be used as well. 
Please look :

Fokine, A. & Urzhumtsev, A.G. (2002) "On the use of low resolution data for 
translation search in molecular replacement". Acta Cryst., A58, 72-74

Fokine, A., Capitani, G., Grütter, M.G. & Urzhumtsev, A. (2003) "Bulk-solvent 
correction for fast translation search in molecular replacement: service 
programs for AMoRe and CNS". J. Appl.Cryst., 36, 352-355.

Best regards,

Sacha Urzhumtsev


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Bernhard Rupp 
(Hofkristallrat a.D.) [hofkristall...@gmail.com]
Envoyé : mardi 3 février 2015 14:49
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Bulk solvent correction in Phaser MR LF

Hi Fellows,

I cannot find the proper reference for the implementation of bulk solvent 
corrections in the
Phaser Molecular replacement likelihood functions.  For the unplaced model, it 
can only be a Babinet model to improve the scaling, and I believe that is 
implemented via a
Babinet rescaled function for sigma A including the coordinate error.

Can anybody help me where to find that?
Thx, BR




Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

2015-02-03 Thread Randy Read
Hi Bernhard,

You're right, it's a Babinet-style correction to the SigmaA curve for the 
effect of neglecting bulk solvent in the model.  We gave a formula in equation 
19 of the main Phaser reference (McCoy et al., 2007), but actually we've 
changed the form of this since then.  It looks like the equation wasn't given 
in the documentation, so I've just updated that:

http://www.phaser.cimr.cam.ac.uk/index.php/Keywords#SOLPARAMETERS

Best wishes,

Randy Read

On 3 Feb 2015, at 13:49, Bernhard Rupp (Hofkristallrat a.D.) 
 wrote:

> Hi Fellows,
>  
> I cannot find the proper reference for the implementation of bulk solvent 
> corrections in the
> Phaser Molecular replacement likelihood functions. For the unplaced model, it 
> can only
> be a Babinet model to improve the scaling, and I believe that is implemented 
> via a
> Babinet rescaled function for sigma A including the coordinate error.
>  
> Can anybody help me where to find that?
> Thx, BR

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk



[ccp4bb] Bulk solvent correction in Phaser MR LF

2015-02-03 Thread Bernhard Rupp (Hofkristallrat a.D.)
Hi Fellows,

 

I cannot find the proper reference for the implementation of bulk solvent
corrections in the

Phaser Molecular replacement likelihood functions. For the unplaced model,
it can only

be a Babinet model to improve the scaling, and I believe that is implemented
via a 

Babinet rescaled function for sigma A including the coordinate error.

 

Can anybody help me where to find that?

Thx, BR