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