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Re: [ccp4bb]: TLS refinement



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Hi

First problem I see is format in range definition. Inside inverted commas 
positions ae important. If you will add one extra space in for instans 
'A 60.' and make it 'A  60.' it may work. If not please let let us know.

Garib
 
On Tuesday 25 Jun 2002 2:59 pm, Thomas Scott Reid wrote:
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>
>
> I am a brand new user of ccp4.  Although weened on CNS, presentations at
> the San Antonio ACA conference has convinced my to try CCP4 for some of my
> refinement, especially TLS refinement in Refmac5.  I can get refmac to
> refine my structure just fine, but the TLS part of the refinement doesn't
> seem to work.
>
> About my project: My crystals contain 6 molecules per asymmetric unit.
> Each molecule is a heterodimer consisting of an alpha and beta subunit
> (molecule 1 = chain A + chain B, mol2 = chain C + chain D, etc., etc.).
> My current model has been fully refined in CNS with Rfree and Rcryst at
> 24.0 and 21.4%.  Waters and ligands are included in the model. My data set
> is complete out to 2.4 A.  The average B factor is ~ 55 A^2. The protein
> N-terminal domains have not been modeled, and some side chains have not
> been modeled because they have no omit density (Is this important?).
>
> I want to see what happens if I add TLS parameters to each of the six
> molecules in the asymmetric unit.  I have not included water or ligands in
> each TLS group (should I?).  The starting TLS input file is as follows:
>
> TLS mol 1
> RANGE 'A 60.' 'A 360.' all
> RANGE 'B 20.' 'B 360.' all
>
> TLS mol2
> RANGE 'C 60.' 'C 360.' all
> RANGE 'D 20.' 'D 360.' all
>
> TLS mol3
> RANGE 'E 60.' 'E 360.' all
> RANGE 'F 20.' 'F 360.' all
>
>
> etc., etc.,
>
>
> I run refmac5 (5 cycles TLS refinement, 5 cycles restrained ML
> refinement), and I see no error messages during the initial TLS refinement
> (with B values fixed at 50 A^2).  Refmac spits out perfectly fine .pdb,
> ...tls and .lib files.  However, during TLS refinement, refmac always picks
> the center of mass for each TLS group as 0,0,0 and assigns TLS values of 0
> for all paramters.  The refined .tls file for the six groups is as
> follows:
>
> TLS mol 1
> RANGE 'A 60.' 'A 360. 'all
> RANGE 'B 20.' 'B 360. 'all
> ORIGIN 0.000 0.000 0.000
> T     0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> L     0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> S     0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
>
> TLS mol2
> RANGE 'C 60.' 'C 360. 'all
> RANGE 'D 20.' 'D 360. 'all
> ORIGIN 0.000 0.000 0.000
> T     0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> L     0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> S     0.0000 0.0000 0.0000 0.0000 0.00000.0000 0.0000 0.0000
>
> etc., etc.,
>
>
> What am I doing wrong?  Its probably something very simple, and related to
> the fact that the PDB file comes straight out of CNS.  Any suggestions
> would be appreciated.
>
>
> Scott Reid
> Dept. of Biochem
> Duke University Medical Center
> tsr@duke.edu

-- 
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 432565