Re: [ccp4bb] refmac Bsol

2011-12-29 Thread Garib N Murshudov
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

2011-12-29 Thread Mike Lawrence
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 !







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[ccp4bb] refmac Bsol

2011-12-29 Thread Bernhard Rupp (Hofkristallrat a.D.)
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

2011-12-29 Thread Antony Oliver
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!