ARP/wARP and SHELXL (#5)

SHELXL is part of the SHELX-97 program package and should be obtained directly from the author, George M. Sheldrick, Göttingen University SHELX homepage.

The most common use of ARP/wARP with SHELXL shelx97 is for restrained refinement with individual atomic anisotropic displacement parameters (as provided by SHELXL) combined with updating of the solvent structure by ARP/wARP . This application is limited to the fact that individual atomic anisotropic displacement parameters can be refined only if the resolution of the X-ray data is higher than 1.5 Å, ideally approaching atomic resolution (1.2 Å).

There are currently no automated scripts for this application. An old-style command shell script is given in the examples/arp_shelx directory. The script includes iterative runs of the following programs:

1.

SHELXL (SHELX-97) for restrained anisotropic refinement
Some recommendations for the shelx.ins file:
CGLS 2. Use of more cycles within SHELXL lowers the ARP_WARP contribution
CELL, LATT/SYMM and SHEL should be consistent with cell, symm and resol in the script
WPDB -1
LIST 3
ISOR and CONN should include O1 > last - as the number of waters changes with each cycle
See the SHELX-97 Manual for further details.

2.

PREPFORM (ARP/wARP Suite) for conversion of SHELXL files

3.

F2MTZ (CCP4) for conversion to the CCP4 MTZ format
Column label assignments should be edited if necessary

4.

CAD (CCP4) for sorting the MTZ file
Column label assignments should be edited if necessary

5.

FFT (CCP4) for map calculation
One map is calculated with coefficients 3Fo-2Fc, another with Fo-Fc Column label assignments should be edited if necessary

6.

EXTEND (CCP4) for map extension

7.

ARP_WARP (ARP/wARP Suite) for solvent update
The maximum number of atoms to add and to remove should not exceed the value of $0.08\times N/d_{max}^3$, where N is the current number of atoms in the model and d_max is the high resolution limit.

8.

PREPSHEL (ARP/wARP Suite) for back conversion to SHELXL format

When writing a shell script take care to define the following variables at the top of the file: name (root file name), last (starting file number), cycles (number of refinement cycles), count, title, resol (resolution limits), cell (cell parameters), grid (grid for map calculation), xyzlim (boundaries for real space asymmetric unit for ARP_WARP), symm (space group number) and sfsg (space group for map calculation)