[ccp4bb]: model bias in refmac5?

[Jinsong Liu <jsliu@tularik.com>]

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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 2.0Å 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
 

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"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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