PyMol Design & Implementation Differences

Moltimate, as PyMol's spiritual successor, has many similarities, but there are a handful of core differences that were made as design choices by the team during the course of development and consultation with the sponsor.

Motif Maker - Custom Tolerance

In PyMol a motif might need its tolerance increased in order to find all of the given residues in the structure (or decrease it when it was finding a similar but incorrect residue). In Moltimate we no longer allow users to increase or decrease the tolerance for a custom motif, due to the differences in how alignments are processed.

In Moltimate we are going through and selecting the residue directly using the identifiers provided and not "looking" for the residue. This means that our motifs can be more accurate and have a consistent tolerance (2 ångströms) during alignment, which can be modified by a precision factor, during a search if desired.

Motif Maker - Backbone Atoms Toggle

In PyMol a motif might require that a specific residue have its backbone atoms turned on (this was off by default since it increased the time of alignment) in order to make the motif more accurate since in some cases the residue could have a similar residue nearby.

In Moltimate we always include the backbone atoms so that we can get a more accurate alignment. Even with this always on, the alignment searches take less time due to other optimizations.