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CCP4BB Home

CCP4BB  March 2009

CCP4BB March 2009

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Subject:

Re: Differences in Refmac5 refinement on CCP46.1.1

From:

Eleanor Dodson <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Mon, 30 Mar 2009 10:24:41 +0100

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text/plain

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Before worrying at the rmsbonds check whether you have some significant 
outliers - these would be listed in the
REFMAC log file. Sometimes these can really distort the quoted values.

  Eleanor

 Anastassis Perrakis wrote:
> Hi Rafael,
>
>
>>
>> Things very different on the "new" version:
>> - The rmsANGL shot up (from 2.088 to 3.088);
>> - The rmsBOND also shot up (from 0.25 to 0.0468).
>>
>> As a consequence of having  my geometric constrains blown up, the Rwork
>> went considerably down.
>>
>> Does anybody have any thoughts on why using the same geometry restraints
>> led to very different results?
>
> From what you show, the logs are not dramatically different anyway. In 
> one case Rfree is 20.37% and in the other 20.4%.
> Which tells you that loosening geometry is not helping ;-)
>
> What you say about the geometry restraints being the same is not correct.
> The relative weight of geometry terms is the same.
> ***But you do not mention anything about the relative weight of Xrays 
> to Geometry, which YOU have to set***
> (new REFMAC has an AUTO version which works OK, but not for the very 
> final rounds, in my opinion)
>
> Would I be right to suspect you have either set the X-ray vs Geometry 
> weight to the wrong value in the old job (0.3 as default?)
> while in the new job AUTO is used?
>
> The rms distance you get in the new job is 0.0468 and the z score is 
> 1.958, clearly indicating that the geometry is far too loose.
> In the old job, you had 0.025 and 2.088, which I also think is loose.
> (unless you have VERY high resolution .. and even then ... I would 
> expect a better zBOND).
>
> Aim for tighter geometry and look at Z-bond (0.5 - 1.0) are good 
> values I think. I personally decided
> I prefer the Ian Tickle analysis btw, and I like looking at the 
> weightB relationship to weightXray.
>
> It was early in the year to have the RMS-bonds discussion... (same as 
> Jim pointed out for the I/sig(I) discussion).
>
>
> Best, Tassos
>
> PS This script can be useful to decide what good weight are (need 
> editing)
> btw, I would love to have that type of Job in ccp4i, and its rather 
> easy to code in Tcl.
> Anybody with time to spare on the CCP4 team ? I think it can be useful 
> to have a job
> for optimizing weights extensively (phenix has also that mode and I 
> like it a lot ... even if its slow).
>
>
>
> #!/bin/csh -f
> #
> echo "xweight bweight rfactor rfree  rmszbonds"  > stats.log
>
> foreach xweight ( 0.04  0.08  0.12 0.16 0.20 0.25 0.30)
> foreach bweight ( 0.1 0.2 0.6 1.0 1.5 2.0 2.5 3.0 )
> #
> # Define your Input / Output files
> #
> refmac5 XYZIN "CLIC3_final_2.pdb" XYZOUT "del.tmp" HKLIN
> "clic3.mtz" HKLOUT "del.mtz.tmp" TLSIN
> "tls_cli3.tls" TLSOUT "del.tls.tmp" LIBOUT "delete.cif" > 
> refmac_${xweight}_${bweight}.log <<EOF
> make check NONE
> make -
>     hydrogen ALL -
>     hout NO -
>     peptide NO -
>     cispeptide YES -
>     ssbridge YES -
>     symmetry YES -
>     sugar YES -
>     connectivity NO -
>     link NO
> refi -
>     type REST -
>     resi MLKF -
>     meth CGMAT -
>     bref ISOT
> refi tlsc 10
> temp set 20.0
> ncyc 10
> scal -
>     type SIMP -
>     reso 2.210 38.691 -
>     LSSC -
>     ANISO -
>     EXPE
> solvent YES -
>     VDWProb 1.2 -
>     IONProb 0.8 -
>     RSHRink 0.8
> weight -
>     MATRIX ${xweight}
> monitor MEDIUM -
>     torsion 10.0 -
>     distance 10.0 -
>     angle 10.0 -
>     plane 10.0 -
>     chiral 10.0 -
>     bfactor 10.0 -
>     bsphere 10.0 -
>     rbond 10.0 -
>     ncsr 10.0
> labin  FP=F_Unspecified SIGFP=SIGF_Unspecified -
>    FREE=FreeR_flag
> labout  FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT 
> PHDELWT=PHDELWT FOM=FOM
> temp ${bweight} 2.0 3.0 2.0 3.0
> PNAME fox
> DNAME 040808
> RSIZE 80
> USECWD
> END
> EOF
>
> echo -n ${xweight} ${bweight} >> stats.log
> awk '(NF=11){if ($1==20) print $2, $3, $8}' 
> refmac_${xweight}_${bweight}.log  >> stats.log
> end
>
> end
>
>

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