Garib,
Yes! That clears it up. The documentation says the default is 1.5 and I
found 1.5 in the source code, so I automatically assumed that was true.
-Billy
On Wed, 14 Feb 2007 18:33:59 +0000, Garib Murshudov <[log in to unmask]>
wrote:
>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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