You didn't say anything about the "weighting term" between the F's and
geometrical parameters. That will substantially affect the R's, and the
default value of 0.3 in REFMAC isn't appropriate for all structures. In
CNS, it's adjusted to a more reasonable value during refinement.
Bernie Santarsiero
On Wed, February 14, 2007 10:36 am, Billy Poon wrote:
> Dear all,
>
> I have been using REFMAC5 to calculate the R values of several structures
> from
> the PDB and was confused by the behavior of the SHANnon_factor keyword.
> When I
> leave it at the default (set at 1.5 in the source code), I get one set of
> R
> values. But when I manually set the value to 1.5 (SHANnon_factor 1.5) in
> the
> script, I get a different set of values. Usually, it's off at the third
> or
> fourth decimal place, but for one case (PDB code 2OAU), I get a difference
> of
> about 0.0116 (0.28416 for default, 0.27258 for manual setting) for the R
> value
> and 0.0184 (0.31653 for default, 0.29818 for manual setting) in the Free
> R.
>
> I have tested this on the following architectures and they all behave the
> same
> way:
>
> Intel Xeon (32-bit Linux, REFMAC 5.2.0019, compiled with Intel compilers
> 9.1)
> Intel Itanium2 (64-bit Linux, REFMAC 5.2.0019, compiled with Intel
> compilers
> 9.1)
> AMD Opteron (64-bit Linux, REFMAC 5.2.0019, compiled with GNU compilers
> 3.3.3)
> SGI MIPS (IRIX 6.5, REFMAC 5.2.0003, pre-compiled binaries)
>
> I am not doing any refining of the structures. I just wanted to see what
> the R
> values are when calculated with REFMAC5 (the structures I was looking at
> were
> refined in CNS or X-PLOR) and was confused by the different results with
> the same setting. Also, should changing the SHANnon_factor affect the R
> values much? Thanks in advance for your help!
>
> -Billy
>
> And the script I use is pasted below:
>
> #
> # Refmac
> #
> refmac:
> refmac5 \
> HKLIN ./fo.mtz \
> XYZIN ./2oau.pdb \
> XYZOUT ./test.pdb \
> << eor
> #
> # Do not add hydrogens
> #
> MAKE HYDR N
> MAKE LINK N
> MAKE CHECK NONE
> #
> # Input mtz labels
> #
> LABIN FP=FP SIGFP=SIGFP FREE=FREE
> #
> # Set resolution
> #
> REFI RESOlution 3.7 50.00
> #
> # Define NCS
> #
> NCSR NCHAI 7 CHAI A B C D E F G NSPANS 1 1 254 4
> #
> # Refine overall B factor
> #
> REFI BREF OVERall
> #
> # Set Free flag
> #
> FREE 0
> #
> # Number of refinement cycles
> #
> NCYC 0
> #
> # Monitoring level
> #
> MONI MEDI
> #
> # Change Shannon sampling (commented out if testing default behavior)
> #
> SHANNON_FACTOR 1.5
> #
> # end
> #
> end
> eor
>
>
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