@JISCMAIL.AC.UKmailto: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
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
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
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
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
Of *Eleanor Dodson
*Sent:* Sonntag, 11. Januar 2015 17:05
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Bulk solvent
Yes. If the model is incomplete it is obviously not sensible to use
the mask based solvent - you will tend to lose the unmodelled
features. It also gives unrealistically low R factors
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor
Dodson
Sent: Sonntag, 11. Januar 2015 17:05
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Bulk solvent
Yes. If the model is incomplete it is obviously not sensible to use the mask
based solvent - you will tend to lose
@JISCMAIL.AC.UK] On Behalf Of Eleanor
Dodson
Sent: Sonntag, 11. Januar 2015 17:05
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Bulk solvent
Yes. If the model is incomplete it is obviously not sensible to use the mask
based solvent - you will tend to lose the unmodelled features. It also gives
Dear Bernhard,
further thinking about the Babinet scaling effects, I have to correct my
conclusion in the last sentence:
On 12.01.2015 14:21, Dirk Kostrewa wrote:
If, however, the unmodelled part is less well ordered (which is the
more common case), it's contribution will mainly affect the
, January 09, 2015 12:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Bulk solvent
Dear all,
Is there any reason for using Babinet scaling for bulk solvent
correction
instead of mask based scaling?
Armando
Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Armando Albert
Sent: Friday, January 09, 2015 12:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Bulk solvent
Dear all,
Is there any reason for using Babinet scaling for bulk solvent correction
instead of mask
] On Behalf Of
Armando Albert
Sent: Friday, January 09, 2015 12:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Bulk solvent
Dear all,
Is there any reason for using Babinet scaling for bulk solvent correction
instead of mask based scaling?
Armando
...@email.arizona.edu
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Armando Albert
Sent: Friday, January 09, 2015 12:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Bulk solvent
Dear all,
Is there any reason for using Babinet scaling
Dear Armando,
Is there any reason for using Babinet scaling for bulk solvent correction
instead of mask based scaling?
in addition to Dirk's excellent comment:
Babinet bulk-solvent model is fine at resolutions lower than 15-20Å while
not so much at higher resolutions as demonstrated by
On 09.01.2015 08:56, Armando Albert wrote:
Dear all,
Is there any reason for using Babinet scaling for bulk solvent correction
instead of mask based scaling?
Armando
Dear Armando,
yes: the mask bulk solvent correction depends on the proper calculation
of a protein mask. The bulk solvent
Dear all,
Is there any reason for using Babinet scaling for bulk solvent correction
instead of mask based scaling?
Armando
Dear Allister Crow,
in cases like these, I would recommend to apply the Babinet bulk solvent
correction instead of the mask bulk solvent correction as a control
(Refmac5 - Scaling - Use Babinet scaling; uncheck Calculcate the
contribution from the solvent region). The Babinet bulk solvent
On Tue, 2012-04-17 at 11:08 +0200, Dirk Kostrewa wrote:
The mask bulk solvent correction is more powerful
Just to note that sometimes Babinet solvent correction returns lower
Rfree and thus may be preferred to mask (assuming that the Rfree is the
only thing that matters).
Beginning with
Dear Allister
Could you please update refmac version. In the version you it seems that bulk
solvent mask calculation has some problems. New version (at the moment) can be
downloaded from this site:
http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz
There is a
Oh dear - this is the version of Refmac in the latest ccp4 release - can
this be updated on the web site as soon as possible ?
Eleanor
On 16 April 2012 12:02, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote:
Dear Allister
Could you please update refmac version. In the version you it seems
Dear Garib,
Is there REFMAC option to output solvent mask information (e.g. Fmask
and PHImask in mtz to check with Coot)?
I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
But I'm not sure that FC_ALL = FC + FMASK is correct or not.
Keitaro
2012/4/16 Garib N Murshudov
Yes there is. If you use command line (it is not available on the ccp4i yet).
If you run with command lines
refmac5 all others like hklin, xyzin etc mskout mask file name eof
all options you want
eof
Then there will be a map and you can visualise it using coot.
regards
Garib
On 16 Apr
A follow up:
In the new version there is FC_ALL_LS, PHIC_ALL_LS
That should be FC_ALL_LS = FC + FMASK.
I have not tried but if you can use vector difference map then it should be:
FMASK = FC_ALL_LS - FC
But it is after scaling. If you write out mask map then it is just 0 1 map (0
inside
:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] bulk solvent treatment inside protein cavities
Dear Garib,
Is there REFMAC option to output solvent mask information (e.g. Fmask and
PHImask in mtz to check with Coot)?
I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL
Dear Garib,
Thank you very much for your quick reply.
I tried mskout option and the output looked almost the same as the map
generated by FC_ALL - FC.
By the way, when mskout option is specified, refmac stops before CGMAT cycles.
Is there any way to do refinement with mskout option?
I have
Dear Ketaro
At the moment mskout option is a signal that the program should stop. Obviously
I can add an option to continue. However if you have mskout option it is likely
that you want to check what is going on with the mask. If you want to compare
starting and final mask then you could run
Dear Garib,
I think it is better if refmac outputs final solvent mask when mskout specified.
If one just wanted to calculate the mask, NCYC 0 should be specified.
I hope my suggestion would be accepted, but I'm not in a hurry.
FC_ALL is ML scaled FC+FMASK
Sometime it may be different from
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