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 <[EMAIL PROTECTED]> 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 >>>> >>>> >>>> >>> >>> >>> >=========================================================================
