Q:

I am currently using your server to morph two actin structures (open nucleotide cleft and closed). Besides morphing the two actin chains, I would also like to morph the bound ATP molecules. Although I can the two actin structures to morph, I cannot seem to figure out how to morph the ATPs. So basically my question is: can bound nucleotides be morphed? How should they be defined in the PDB filem which server to use, and should the morphs be done separately (i.e. protein and ATP as separate morphs)?

A:

Thank you for your query, and for using MolMovDB. Specifically, which server is it that you have been using, and what error message(s) are returned? It is sometimes the case that the formatting of the PDB files must be manually changed in certain ways, and this in and of itself can be a little tricky. If you like (and if you don’t mind), you may send the PDB files to me, and I will spend some time on trying to format them for the server. If all else fails, it may indeed be necessary to morph things separately, but combining the resultant morphs may be an endeavor on its own.

Finally (and importantly), I should point out that the PDB formats may not be the issue at all; it may be the case that that there is an issue with ATP constituting ‘heteroatoms’. Dealing with heteroatoms in our server is extremely difficult, and this is sometimes a result of the way in which they’re numbered in your input files. In addition, parameterizing heteroatoms using our interpolation software is very difficult (to the point that, if you do indeed obtain a morph, the resultant interpolation may be very questionable, so it may be a use-at-your-own-risk practice if the parameterization is not done properly).