Re: [ccp4bb] refmac Bsol
Partial structure mask bulk solvent parameters. If you use simple scaling then mask solvent is still on. You can turn it off by "Calculate the contribution of from the solvent region" To turn Babient's bulk solvent you need to use Babinet's scaling instead of simple. I hope it helps regards Garib On 29 Dec 2011, at 21:08, Bernhard Rupp (Hofkristallrat a.D.) wrote: > Dear Refmac developers group, > > I am trying to understand a small detail in the refmac log listing. In the > bulk > > solvent section just below the restraint table (I use monitor MANY in > general): > > - > > Overall : scale =0.891, B = -0.266 > > Partial structure1: scale =0.375, B = 24.388 > > Overall anisotropic scale factors > >B11 = -0.39 B22 = 0.09 B33 = 0.33 B12 = -0.00 B13 = 0.48 B23 = 0.00 > > - > > > Is the listing indeed containing the flat bulk solvent model (‘simple model’ > in refmac gui, SOLVENT YES) k and B in the first 2 lines? > > > If so, I am curious > > a) what exactly is ‘Overall’ versus ‘partial structure’? What is the > relative magnitude of the scale and B telling me in each case? > > b) would it not be useful to have it reported in the PDB header? > > All I find there is the anisotropic B scaling matrix and a mean (overall) B > value (of unspecified origin – how exactly is that computed?) > > REMARK 3 B VALUES. > > REMARK 3 FROM WILSON PLOT (A**2) : NULL > > REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.711 > > > Explanation/intuition would be much appreciated. > > > Best regards, BR > > - > > Bernhard Rupp > > 001 (925) 209-7429 > > +43 (676) 571-0536 > > hofkristall...@gmail.com > > b...@hofkristallamt.org > > http://www.hofkristallamt.org/ > > -- > > Old and treacherous will beat young and skilled every time > > -- > > PS: The doc leaves me a little confused because SCAL type SIMP would imply > > KB = K0*exp(-B0*s^2) (Simple Wilson scaling) > > i.e. K1 = 0 > > while BULK (Babinet) which I did not specify > > KB = K0*exp(-B0*s^2) * (1- K1*exp(-B1*s^2)) > > gives me 2 Ks and Bs. > > So I conclude that ‘overall’ and ‘partial’ lines do not list Babinet ks and > Bs (the B is also too small for that) > > Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] Help me install O on ubuntu11.10
Try sudo apt-get install ia32-libs lib32gfortran3 to install the required 32 bit libraries On 26/12/2011, at 9:53 PM, 王瑞 wrote: > Excuse me, could anyone can tell me how to install O on ubuntu11.10 ?Thanks a > lot ! __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __
[ccp4bb] refmac Bsol
Dear Refmac developers group,
I am trying to understand a small detail in the refmac log listing. In the
bulk
solvent section just below the restraint table (I use monitor MANY in
general):
-
Overall : scale =0.891, B = -0.266
Partial structure1: scale =0.375, B = 24.388
Overall anisotropic scale factors
B11 = -0.39 B22 = 0.09 B33 = 0.33 B12 = -0.00 B13 = 0.48 B23 = 0.00
-
Is the listing indeed containing the flat bulk solvent model ('simple model'
in refmac gui, SOLVENT YES) k and B in the first 2 lines?
If so, I am curious
a) what exactly is 'Overall' versus 'partial structure'? What is the
relative magnitude of the scale and B telling me in each case?
b) would it not be useful to have it reported in the PDB header?
All I find there is the anisotropic B scaling matrix and a
mean (overall) B value (of unspecified origin - how exactly is that
computed?)
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.711
Explanation/intuition would be much appreciated.
Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
hofkristall...@gmail.com
b...@hofkristallamt.org
http://www.hofkristallamt.org/
--
Old and treacherous will beat young and skilled every time
--
PS: The doc leaves me a little confused because SCAL type SIMP would imply
KB = K0*exp(-B0*s^2) (Simple Wilson scaling)
i.e. K1 = 0
while BULK (Babinet) which I did not specify
KB = K0*exp(-B0*s^2) * (1- K1*exp(-B1*s^2))
gives me 2 Ks and Bs.
So I conclude that 'overall' and 'partial' lines do not list Babinet ks and
Bs (the B is also too small for that)
Re: [ccp4bb] Superpose problem
You could use the Superpose program to generate superpositioned/superposed/superimposed models - i.e. to put your structures on top of each other. There are also a host of other programs available to do the same thing (!) In Phaser, you would then load each of these superimposed models, to generate your search "ensemble". The words superposition, superimposition, and superpose, to all intents and purposes mean the same thing (ducks behind flame-resistant wall). With regards, Tony. Sent from my iPhone On 29 Dec 2011, at 06:16, "SUBSCRIBE CCP4BB Huo tong" wrote: > Hello everyone: > I am just learning how to use the CCP4 Program suite. When I use the MR > approach --Phaser, there is a column say > "Add superimposed PDB file to the ensemble". And there is another CCP4 > supported program called "Superpose". > I am afraid if my question is professional, but I wonder > 1)if there is any differences between "Superpose" and "Superimpose"; > 2)when to use the Superpose or Superimposed function > > Any answer is welcomed!
