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
>>>
>>>
>>>
>>
>>
>>
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