On 8/9/12 7:53 AM, Marco Lolicato wrote:
I've already had a look into the forum but I didn't find the answer. I would like to model a chimera protein where the two segments are deposited into the Protein DataBank. One of the two proteins is a membrane protein. I used the default values with really interesting results, but I guess I have a problem in modeling the soluble portion of the chimera: in fact, in the model, it appear in the same orientation of the transmembrane helices of the membrane portion. It seems that the soluble portion itself can insert in the membrane.
Models generated in Modeller will always resemble the template, so you can definitely model membrane proteins, provided you have a membrane protein template - you don't need to do anything special. If the model does *not* look like the template, your alignment is probably incorrect (it sounds here as if you have aligned the soluble portion with the transmembrane portion by mistake).
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage