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