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Re: [ccp4bb]: model bias in refmac5?



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Just want to add one more thing. I am pretty sure I was not calculating
FC map, I used F1=FWT, PHI=PHWT in fft. Though I didn't specificly  put
FWT and PHWT in the LABOUT of refmac5, but that should be the default?
Am I wrong?

Jinsong

Jinsong Liu wrote:
> 
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Dear All,
> 
> I would like to get some opinions from people using refmac5 about how
> serious the model bias the map coefficient (FWT, PHWT) would be.
> 
> I have a low resolution data, complete to 96% at 3.7A. Using molrep, I
> get different solutions from different homology models. Then I put these
> models in refmac5 for one cycle of rigid body (I got two molecules per
> ASU, each one as one rigid body) to calculate a 2fofc map. In most
> cases, the map looks too good to be true. But remember, these are all
> different MR solutions and only one can be real. I even throw in a
> totally different protein for Molrep, and refmac5, the map looks
> beautiful.
> 
> The R-factor for those refmac are around 51%-53% range, considered the
> model is only about 1/3 of the total size of the protein I am working on
> this R-factor is not too bad for this resolution.
> 
> Using exact same script, refmac (instead of refmac5) generated a worse
> map , though I can still see obvious model bias.
> 
> Using CNX model_map.inp, the calculated map is unthinkable for one case
> I tested, that is clearly not my solution based on the map.
> 
> In my memory, refmac map showed very little model bias except there are
> lots of missing data which is not the case I have here. This is the
> first time I saw such a heavy model bias in refmac. I used the standard
> script from the refmac5 example which is at the end of this mail.
> 
> Can anyone give me some hints?
> 
> Thanks
> 
> Following is the rigid.csh script I used:
> 
> refmac5 \
> HKLIN $inmtz \
> HKLOUT ${name}${curr}.mtz \
> XYZOUT ${name}${curr}.pdb \
> XYZIN ${name}${last}.pdb    \
>    << eop>${name}${curr}.log
> #
> #   Input mtz labels
> LABI FP=F SIGFP=SIGF FREE=FreeR_flag
> LABOUT FC=FC PHIC=PHIC
> #
> #    Refinement parameters. Maximum likelihood refinement.
> #    Reflections between 15 and 2.0 will be used
> #
> REFI TYPE RIGID RESI MLKF RESO  20  4.0
> #
> #   Scaling parameters. For rigid body sometimes bulk solvent based
> #   on constant value could be switched off
> #SOLVent NO
> #
> #    Fixing Babinet's bulk solvent parameters sometimes helps to
> #    stabilise scaling
> #
> SCALe TYPE BULK LSSC ANIS FIXBulk BBULk 200.0
> #
> #   Rigid body parameters
> #
> #   Number of cycles
> #
> RIGIdbody NCYCle 1
> #
> #   Domain definition. Each group is one rigid body. It may consist of
> #   several unconnected pieces of chain
> #
> RIGIdbody GROUp 1 FROM 285  A TO 453  A
> RIGIdbody GROUp 2 FROM 285  B TO 453  B
> 
> #
> #   First cycle will give R, free R over resolution. Last cycle also
> #   will give rotation matrices and angles and translations
> #
> NOHARVEST
> MONI MEDIum
> END
> eop
> 
> 
> --
> -----------------------------------------------------------------------
> "The DAO is not a real DAO when it can be talked about."
>                                                 ---(DAO DE JING)
> Jinsong Liu, Ph.D.
> Tularik Inc.                            Phone:  650 825-7054
> Two Corporate Drive                     Fax:    650 825-7320
> South San Francisco, CA 94080, USA      Email: jsliu@tularik.com
> -----------------------------------------------------------------------

-- 
-----------------------------------------------------------------------
"The DAO is not a real DAO when it can be talked about." 
						---(DAO DE JING)
Jinsong Liu, Ph.D.                                   
Tularik Inc.				Phone: 	650 825-7054
Two Corporate Drive         		Fax: 	650 825-7320
South San Francisco, CA 94080, USA	Email: jsliu@tularik.com
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