Page Comparison

...

Select a template and make a model. Make sure you have the GPCR class A alignment selected. Use Yasara or Pymol to open it. Making the model may take a few minutes. If 3DM wasn't able to model parts of the sequence, these parts will be missing in your model. These missing positions are indicated as purple dots in Yasara and as lines in Pymol. Usually this is because the alignment between the sequence and the template cannot reliably be made (often the parts outside the core) due to very low sequence similarities. Realize that those parts cannot be modeled reliably using the selected template, because the sequence similarity is so low that the two proteins will likely fold differently in those parts. Sometimes it helps making a model choosing a different template (if available), but usually this means that those parts can simply not be modeled reliably.

If 3DM wasn't able to model parts of the sequence, you will see purple dots in Yasara. Usually this is because the alignment between the sequence and the template cannot reliably be made (often the parts outside the core) due to very low sequence similarities. Realize that those parts cannot be modeled using this template because if the sequence similarity is so low the two proteins will likely fold differently in those parts. Sometimes it helps making a model choosing a different template (if available), but usually this means that those parts can simply not be modeled reliably.

...