Quick Start III-1.    Quick Heavy-Atom Sites Searching with Parallel SHELXD

 

{0}.     i) Log on to the cluster using: ‘ssh  –X  username@idc11’.

  ii) Go to the directory with your *.sca data file(s).

 iii) sgxpro

 

·       Try login as ‘staff’ and copy/scp your ‘.sca’ file there, if your account on the cluster has problems.

 

Searching heavy atom sites is the first step in novel-structure-solving process.  The newly developed Parallel SHELXD module in SGXPRO would quickly (in a couple of minutes on the cluster) tell if there is any anomalous signal or the anomalous signal is good enough to find heavy atoms.  If not, you might have to check your data collection (wavelength, beam intensity, exposure time, redundancy …), data processing etc. to find and solve those experimental problem(s) that you can’t do anything about after your data collection is done.

 

B

 

E

 

D

 

C

 

A

 

 

A. Click on “HA Search”, then “Parallel ShelxD” buttons to bring up SHELXD GUI.

B.  Browse your .sca file (output from HKL2000 with anomalous on) or .hkl file of

      the SHELX HKLF 3 format.  Check to make sure the space group is right (‘spgr4d’

      can help).

C. Select heavy-atom type, and give the number of sites (in one AU) to search.  If totally

      unknown as in cases of soaked derivatives, give a reasonably larger number. 

      SGXPRO has a built-in algorithm to output the only sites that are reasonable.

D. Click on “Save” button.

E. Click on “Run” button.

 

Results: The ‘*.shelxd.log’ contains the best “CC all/weak” (an above

                 30/above 10 is a good sign).  The HA site(s) if found are saved in

                 the ‘*.xyz’ file in PDB format.

 

Ref: Fu, Chrzas, Sheldrick, Rose, Wang (2007):  J. Appl. Cryst.   40: 387-390.

 

 

 

 

 

Quick Start III-2.    Evaluate Anomalous Scattering Data Quality with Ras

 

{0}.     i) Log on to a computer (using ‘ssh –X’ when remotely).

  ii) Go to the directory with your *.x files.  Run command:

                 spgr4d  Npix  startXfile  [Nframes]  ras  SP

 

Example:

spgr4d  4000  test_1_0001.x  ras  p41212

 

This command will use all frames of data set 'test_1_####.x' to evaluate the anomalous signal/noise ratio with space group P41212.  The number ‘4000’ is the detector dimension in pixels of MARCCD300, on which the data were collected.

 

For more details on how to use the program, just type the command spgr4d from a terminal.

 

Notes to SER-CAT Users:  SGXPRO is available on all the SER-CAT computers for data processing.  Functions like Ras evaluation described in this section and other utility tools can be done on any of these computers.  To reduce the workload, please use the cluster only if it is necessary.

 

About the Results:

Based on tests, a to-shell (cumulated) Ras of 1.5 may be significant and have a good potential for successful phasing with most of the current heavy-atom searching and phasing computer programs.  The larger, the better.  However, if the in-shell values are very bumpy, it may not be good enough.  Statistically, the anomalous signal-to-noise ratio decreases with resolution.  So, a smoothly decreasing Ras with resolution is expected for a normal data set.  If the Ras values in the resolution shells are significantly up and down, it may suggest a low redundancy etc..

 

Tips:

1). The ‘.merx’ data file output from spgr4d can be read into SGXPro -> Data Reduction -> 3DScale, where more control options (such as resolution cutoff) are available.

2). Data integrated by programs such as d*Trek, Proteum etc. can be directly input into 3DScale as in Tips 1).

 

Warning: The ‘spgr4d’ calls ‘merx’ to harvest reflections from .x files, then ‘3DSCALE’ for scaling.   As ‘merx’ is a very simple program lack of post-refinement to appropriately merge partial reflections, the merged data in ‘.merx' file are not accurate, leading to the scaled data that are not the best you could get from 3DSCALE.  However, Ras calculated using the data harvested by ‘merx’ is found reliable based on the tests done so far.

 

Ref: Fu, Z.-Q., Rose, J. & Wang, B.-C. (2004): Acta Cryst. D60:499-506.

 

 

 

 

 

Quick Start V.     Other Utility Tools

 

SGXPRO has many other modules and built-in utility tools.  For example, the ‘FpFpp’ utility tool provides an  f’, f’’ vs energy/wavelength plot of any selected atom/ion type, providing a general idea what the anomalous scattering looks like, what anomalous signal level you would expect for a certain heavy-atom type etc., which may help selecting a wavelength and planning your data collection ahead of a trip.  Shown bellow is the plot for Ho.

 

Click on the curve will point to the corresponding data values in the table on the left.
 

 

 

Ref: Fu, Z.-Q., Rose, J. & Wang, B.-C. (2005): Acta Cryst. D61:951-959.