Hi all, I am increasingly dealing with large macrocycles or cyclized peptides that include unnatural amino acids or modifications. Early on my approach was to treat most of it as the native peptide scaffold, then add a few custom 'LINK' records to capture covalent bonds to some non-native moiety, and that moiety would be defined as we do for small molecule synthetic ligands. Advantage was that it was efficient for refinement of the conventional amino acid scaffold. Disadvantage, a bit cumbersome and I do find that while the covalently bonded attachment point is reasonable, the neighboring atoms to that new attachment don't always behave reliably (as in perhaps don't have the knowledge that their neighbor has something new attached which affects their space.) As our chemists got more creative, it also is tedious to sit there trying to make 5 or 6 little bits and pieces that all have to be attached to different atoms along the scaffold. Plus the bookkeeping of made up names for little extra ethylenes, halognes, and their atom name attachment points and such was pretty painful.
So, that led to approach two, which was to just let the dictionary generation happen for the whole peptide or macrocycle. This ignores knowledge that it's essentially an amino acid type of base scaffold (so a bit inefficient for purists) and just redefines all those as if it's some small molecule, albeit a relatively large version of one of those. You also lose residue number indexing, as the whole thing is typically called "LIG" with a single residue identifier, but it seems a small price to pay for the convenience of it taking care of all the sundry modifications and cyclization points, etc. The problem I'm having is that COOT is having trouble reading or using these large .cif files. The files may be 1000 or more lines long with the hydrogens defined. I've tried dropping all hydrogens but it's still large and when I go to real space refine or do any editing to move the starting conformation of the molecule in question into the clear density for it bound to some protein, Coot basically hangs either indefinitely or for several minutes at a time at least with each attempted motion, step. Is there some memory allocation for the .cif dictionary that perhaps is limiting? I don't have a handy non-proprietary example currently, but could likely generate one if needed. Or have people had success with this approach (e.g. taking a 10-14 amino acid peptide, treat it as a SMILES string and generate a .cif for the whole thing as a single molecule and then be able to use it in real space refinement in Coot? ) I've tried a few workarounds to get the atoms pretty close and then let reciprocal space refinement do the rest, but there really aren't so many good ways to do that (Pymol's sculpting drifts, was playing with Isolde but having similar technical issues with the restraints definitions). Thanks for thoughts, or info on Coot and large .cif dictionaries? Cheers, Seth ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
