There re two places where FSHANN is set. One when keyword is read and
one default initial value. The second value is the default.
The first set is when you make mistake with the keyword and the
second one is the default. Is this what you have?
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
rcard_tor1.f:c----Read shannon factor for grid spacing. Fshann is
factor by which
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
rcard_tor1.f: FSHANN = 1.5
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
rcard_tor1.f: CALL GTNREA(2,1,FSHANN,NTOK,ITYP,FVALUE)
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
rcard_tor1.f: IF(FSHANN.LE.0.0) THEN
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
rcard_tor1.f: FSHANN = 1.5
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
rcard_tor1.f: ELSEIF(FSHANN.LE.1.0) THEN
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
rcard_tor1.f: FSHANN = 1.0/FSHANN
/Users/garib/ccp4_ibm/ccp4_5.0.2/ccp4-5.0.2/src/refmac5_/
rcard_tor1.f: FSHANN = 1.4
Garib
P.S. That is for version 5.2.0005. For the next version it will be
1.5 (it seemed to give consistent results).
On 14 Feb 2007, at 18:24, Billy Poon wrote:
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
