• It might be a good idea to run these tutorials in a fresh directory on your system, e.g. via
       mkdir -p ~/Projects/autoSHARP/Tutorials
       cd ~/Projects/autoSHARP/Tutorials
  • After downloading the relevant data files (sequence, reflection, initial model PDB etc) via "[right mouse click] -> Save Link As ...", it might be necessary to move them into the current working directory. Often, the browser will save downloaded files in ~/Downloads and you could use e.g.
       mv ~/Downloads/1o22* .
  • The commands shown below could be used as-is with the provided files - just cut-n-paste them into your terminal window:
    • mark the full command via the left mouse button, move the mouse into your terminal window and then press "[middle mouse]". If this doesn't work, use the normal "Copy" and "Paste" functionality.
    • the "\" character marks a continuation and therefore is part of the command
  • Each of those commands will write some information into your terminal ("standard output") - among them the name of a HTML file ("LISTautoSHARP.html"). You should open this HTML document into a browser (Firefox, Chrome, Safari etc) and reload it from time to time while the program is still running and writing to this file.
  • The timings given below are for a reasonably fast computer with 4 threads: this might be faster for more modern and powerful machines or slower when running on some old hardware.
  • Most of the time will be spent in automatic model building and density modification (the actual HA substructure solution, completion and phasing typically takes only 2-10 minutes in most cases).
  • The automatic building can be skipped by adding "-nobuild" to the command-line (but this might not give as good density).

SAD (single wavelength)


SAD-1 (1O22): \
          -seq 1o22.pir -ha "Se" \
          -wvl 0.9778 peak -7 5 -sca \
          -id autoSHARP_SAD-1 | tee autoSHARP_SAD-1.lis

      # or: -seq 1o22.pir -ha "Se" -wvl 0.9778 peak -7 5 -sca -id autoSHARP_SAD-1 | tee autoSHARP_SAD-1.lis

SAD-2 (4J8P): \
          -seq 4J8P.pir -ha "Se" \
          -wvl 0.97858 peak -8.000 6.000  -mtz 4J8P_truncate.mtz \
          -id autoSHARP_SAD-2 | tee autoSHARP_SAD-2.lis

SAD-3 (4HPE): \
          -seq 4HPE.pir -ha "Se" \
          -wvl 0.9794 peak -7.963 5.573  -mtz 4HPE_truncate.mtz \
          -id autoSHARP_SAD-3 | tee autoSHARP_SAD-3.lis

MAD (multiple wavelength)

Of course, any of these MAD examples could also be run as SAD, i.e. using only one of the wavelegnths. Some should still work in those cases, while others might not. It might be a good experience, to try different combinations of SAD and/or MAD (e.g. 2 versus 3 wavelengths) to see the effect on HA substructure solution, phasing, density modification and final automatic building.

MAD-1 (3ISY): \
          -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-1 | tee autoSHARP_MAD-1.lis

MAD-2 (4JM1): \
          -seq 4JM1.pir -ha "Se" \
          -wvl 0.97849 peak -4.660 4.060  -mtz 4JM1_truncate_0.97849.mtz \
          -wvl 0.97917 infl -7.690 2.050  -mtz 4JM1_truncate_0.97917.mtz \
          -id autoSHARP_MAD-2 | tee autoSHARP_MAD-2.lis

MAD-3 (4IS3): \
          -seq 4IS3.pir -ha "Se" \
          -wvl 0.97936 infl -11.400 3.710  -mtz 4IS3_truncate_0.97936.mtz \
          -wvl 0.91162 hrem  -1.700 3.300  -mtz 4IS3_truncate_0.91162.mtz \
          -wvl 0.97919 peak  -8.700 6.670  -mtz 4IS3_truncate_0.97919.mtz \
          -id autoSHARP_MAD-3 | tee autoSHARP_MAD-3.lis

MAD-4 (4ME8): \
          -seq 4ME8.pir -ha "Se" \
          -wvl 0.97944 infl -8.600 2.660  -mtz 4ME8_truncate_0.97944.mtz \
          -wvl 0.91837 hrem -1.800 3.400  -mtz 4ME8_truncate_0.91837.mtz \
          -wvl 0.97894 peak -6.860 4.580  -mtz 4ME8_truncate_0.97894.mtz \
          -id autoSHARP_MAD-4 | tee autoSHARP_MAD-4.lis

Using an initiual (partial) model, e.g. from MR solution

autoSHARP allows the use of an input (already placed) model for any phasing scenario - in which case the de-novo HA substructure finding step (with SHELXC/D) is skipped and HA sites are found based on the initial phases from this model (via LLG residual maps in SHARP). Such a model could e.g. be an initial MR solution that is not accurate enough to allow refinement or only one component of a hetero-multimer could be placed. There are a variety of situations, where some meaningful initial PDB model is available. This model and the reflection data given to autoSHARP should have the same (correct) spacegroup as determined through the steps leading to the initial model.

MR-1 (3GET): \
          -seq 3GET.pir -ha "Se" \
          -pdb 3FFH_ala_MR.pdb \
          -wvl 0.9789 peak -8 4 -sca \
          -id autoSHARP_MR-1 | tee autoSHARP_MR-1.lis

SIRAS (native plus single derivative)

This could also be run as SAD, using only the derivative dataset.

SIRAS-1 (1GXT): \
          -seq 1GXT.pir \
          -nat -mtz 1GXT_nat.mtz \
          -ha "Hg" -nsit 2 -wvl 0.99970 peak -16 10 -mtz 1GXT_hg.mtz \
          -id autoSHARP_SIRAS-1 | tee autoSHARP_SIRAS-1.lis

MIRAS (native plus multiple derivatives)

This could also be run as SIRAS using only one of the derivative soaks.

MIRAS-1 (3ZFT): \
          -seq 3ZFT.pir \
          -nat -mtz 3ZFT_nat.mtz \
          -ha "Hg" -nsit 1 -wvl 1.54179 -mtz 3ZFQ_Hg.mtz \
          -ha "Ir" -nsit 2 -wvl 1.54179 -mtz 3ZFR_Ir.mtz \
          -id autoSHARP_MIRAS-2 | tee autoSHARP_MIRAS-2.lis