Thanks both for your quick replies!
Bernie,
I didn't use the WEIGHT keyword because I'm not doing any refinement. I
only want to calculate the R values for a structure without any
minimization. And it seems that setting the SHANnon_factor keyword to
the default value gives different R values than not setting the
SHANnon_factor keyword at all (the program will use the default value in
the source code).
And Garib,
In rcard_tor1.f in the $CCP4/src/refmac5_/ directory, the default
shannon factor seems to be set to 1.5. I'm using version 5.2.0019 of
REFMAC. Is the default something else in the newer version?
-Billy
Santarsiero, Bernard D. wrote:
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
