Here we will collect some information regarding use of our software (during tutorials or when using it on your own) that is particular to the setup during the DLS-CCP4 Data Collection and Structure Solution Workshop (December 13-20 2016).

We will try and keep this page here up-to-date as we get settled in during the course.


You might need to load a so-called module (every time you open a shell/terminal):

% module load ccp4-workshop
% module load sharp

NOTE: the current version of SHARP installed here is from September 2015, so not quite up-to-date. We are trying to fix that asap, but be prepared for some potential side-effects and issues.

There are different ways of running autoSHARP:

  • from within the CCP4i (not yet in CCP4i2) there is an autoSHARP task in
      Experimental Phasing
        --> Automated Search & Phasing
              --> autoSHARP
    • this has the advantage for users of CCP4i of presenting a familiar interface
    • however, looking at resulting maps and models requires a bit more work (one needs to download/save files first before loading them into Coot)
    • when loading MTZ files from SHARP/autoSHARP into Coot you need to select the correct columns for the type of map you want to look at (see here for details if the column naming is not already obvious
    • please ensure that you have configured CCP4i correctly to use your browser of choice (e.g. firefox) as so-called "hypertext" viewer
  • if you can type -h in a terminal (and it comes back with the help message), then everything should be setup correctly for using the command-line interface to autoSHARP. You might want to have a printout of the autosharp_reference_card.pdf handy to help with usage.
    • this interface has the advantage of creating (at the end) little scripts to present results from various stages of structure solution easily within coot. You can run those using e.g.
          % coot --script 04_coot.scm

Example datasets and tutorials

There are several examples and tutorials available, e.g.

  • some suggested runs could be (to be faster - depending on the speed of the computing hardware at the course - just add the flag "-fast" to the command line: those jobs should still work fine with this):
          % -seq 1o22.pir -ha "Se" \
                             -wvl 0.9778 peak -7 5 -sca \
                             -id autoSHARP_SAD | tee autoSHARP_SAD.lis
          % -seq 3isy.pir -ha "Se" \
                             -wvl 0.97934 infl -11 3.3  -sca \
                             -wvl 0.91162 hrem -1.8 3.3 -sca \
                            -id autoSHARP_MAD | tee autoSHARP_MAD.lis
    • MIRAS: 3ZFT.pir (this can run for a bit longer, but when running with the -fast switch it is possible the refined phases are not good enough for interpretation of density)
          % -seq 3ZFT.pir \
                             -nat -sca \
                             -ha "Hg" -nsit 1 -wvl 1.54179 -sca \
                             -ha "Ir" -nsit 2 -wvl 1.54179 -sca \
                             -id autoSHARP_MIRAS | tee autoSHARP_MIRAS.lis
  • or use your own data, especially if you have
    • a sequence file (see here for format description)
    • a reflection file (ideally a merged *.sca file, e.g. from running autoPROC)
    • information about heavy atom(s) (number, f'/f'' etc)