Re: [modeller_usage] Multiple Sequence Alignment vs Single Alignment

On 7/21/11 12:16 AM, Daniel Li wrote: > From reading it seems as if multiple templates should usually generate > better scores but running 3 trials of 600 with different sets of > templates for different proteins I still get better results from my > single template models. So is there something I have to manipulate with > the scripts and parameters?

Multiple templates generally do give better models, but they are more sensitive to alignment errors - the templates have to be quite well aligned with each other, otherwise they will present conflicting information (e.g. one template says that a given CA-CA distance is 5 angstroms, and another 10 angstroms) which is difficult to satisfy.

Ben Webb, Modeller Caretaker