On 7/17/11 10:57 PM, richard k belew wrote:
i've done a couple of runs using the ModWeb server, and i'm wondering how to recapitulate its results using Modeller directly? ModWeb gives a .pdb file as a result, with a header that tells the template it selected, and regions in it that were used for modeling. but: - what method is used for selecting this template? - is it possible to get the alignment that was used?
If you asked for your results to be uploaded into ModBase, you can download the alignment file for each model from that web interface. The header of the alignment file specifies the method that was used to find the template (e.g. sequence-sequence, sequence-profile).
If you instead chose to have the models sent directly to you, the alignment file isn't available. But it might still be on our system somewhere - if you email modweb@salilab.org with your ModWeb job ID we can see if we can find it for you.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage