On 11/21/2012 08:08 AM, sdimicco wrote: > 1) As I changed the optimization protocol, I woul dlike to check if my > set up has been done. Where could I check it?

I'm not sure what you mean here. Look in the log file?

> 2) I am building a multimeric protein. The DOPE and GA341 scores are > developed for single chain models. How can I asses the quality of my > models? The sole molpdf is sufficient?

molpdf just shows you how closely the model satisfies the restraints. It doesn't tell you whether the restraints themselves encode for a good model. We don't have any assessment scores that are tested on multimeric proteins.

> 3) I found thie messagge in the log file: > > Treating residue type GSH as a BLK (rigid body) > even though topology information appears to be at least > partially available. To treat this residue flexibly > instead, remove the corresponding 'MODELLER BLK RESIDUE' > REMARK from the input PDB file. > > I have understood that the input PDB file is the .ini, which is written > during the calculation. Thus, how can I "remove the corresponding > 'MODELLER BLK RESIDUE" to treat the residue flexible? Have I to define > it as my own residue?

If you want to treat the residue flexibly, add its one-letter code to your alignment rather than using the '.' code. For most ligands, '.' (BLK) is quite sufficient, however.

Ben Webb, Modeller Caretaker