Manually remove all waters other than those you wish to be included in the calculation. Manually remove all waters other than those you wish to be included in the calculation. Make sure to untick the "Remove waters" checkbox during the protein preparation stage. Each remaining water molecule will need to be protonated in the context of the binding site, i.e. have its hydrogen atoms in the correct orientation. Each remaining water molecule will be treated just like the protein atoms, and no maps will coincide with the water's position.
Only calcium, magnesium and zinc atoms are currently supported. If your protein contains one of these metal centres, select it to be included in the calculation in the "Include Ligands" dropdown menu at the protein preparation stage.
Under Protonation States, could it please say the following: The "Add Hydrogens" feature of the protein preparation stage uses the CSD Python API, but it cannot be guaranteed that the protonation states of side chains are correct. Terminal protein OH, NH3 and SH groups are rotatable, however histidine, asparagine and glutamine sidechains will not be flipped. The safest approach is to first protonate your protein, manually check the protonation states are sensible, then submit the job with "Add Hydrogens" unticked.
Very large proteins can make the initial SuperStar step much slower. Once it completes, the large grid files from SuperStar can cause the Fragment Hotspot Maps to hit the memory limit. To speed up the calculation, and make it more likely to finish, remove any unnecessary chains or submit them as separate jobs.
To keep this web tool simple, a log in system has not been implemented. This means that all results are pooled together in the Results table. Only the 100 most recent results will be kept.
If you have any other problem or enquiry, please contact us at support@ccdc.cam.ac.uk