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. The waters will need to be protonated in the context of the binding site, i.e have its hydrogen atoms in the correct orientation. The 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.
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 groups OH, NH3 and SH are rotatable, however histidine, asparagine and glutamine side chains will not be flipped. The safest approach is to first protonate you protein, manually check the protonation is sensible, then submit the job with "Add hydrogens" unchecked.
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. Results will only be kept for a certain amount of time. It is also possible for any user to delete any job, but it is assumed that everyone can be trusted.
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