Content:

Notes:

       mv ~/Downloads/1o22* .

SAD

 

SAD-1 (1O22):

      run_autoSHARP.sh \
          -seq 1o22.pir -ha "Se" \
          -wvl 0.9778 peak -7 5 -sca 1o22_peak.sca \
          -id autoSHARP_SAD-1 | tee autoSHARP_SAD-1.lis

      # or:

      run_autoSHARP.sh -seq 1o22.pir -ha "Se" -wvl 0.9778 peak -7 5 -sca 1o22_peak.sca -id autoSHARP_SAD-1 | tee autoSHARP_SAD-1.lis
 

SAD-2 (4J8P):

      run_autoSHARP.sh \
          -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):

      run_autoSHARP.sh \
          -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):

      run_autoSHARP.sh \
          -seq 3isy.pir -ha "Se" \
          -wvl 0.97934 infl -11 3.3  -sca 3isy_aimless_0.97934A.sca \
          -wvl 0.91162 hrem -1.8 3.3 -sca 3isy_aimless_0.91162A.sca \
          -id autoSHARP_MAD-1 | tee autoSHARP_MAD-1.lis
 

MAD-2 (4JM1):

      run_autoSHARP.sh \
          -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):

      run_autoSHARP.sh \
          -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):

      run_autoSHARP.sh \
          -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):

      run_autoSHARP.sh \
          -seq 3GET.pir -ha "Se" \
          -pdb 3FFH_ala_MR.pdb \
          -wvl 0.9789 peak -8 4 -sca 3GET.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):

      run_autoSHARP.sh \
          -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):

      run_autoSHARP.sh \
          -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