Questions about alignment and stereo clashes
Dear Modeller Users,
Hope this email finds you well! I’m recently working on homology modeling of Dopamine D1 receptor. Can I ask two questions?
1. Am I able to use the sequence alignment from external sources, like Blast?
2. When the model was built, I found many stereo clashes in the structure. Is this normal? Is there any way that I can fix the stereo clashes?
Thank you so much, Haoxi
On 3/30/20 11:15 AM, Li,Haoxi wrote: > 1. Am I able to use the sequence alignment from external sources, > like Blast?
Of course. Modeller doesn't care where the alignment comes from, as long as it's in the correct format.
> 2. When the model was built, I found many stereo clashes in the > structure. Is this normal? Is there any way that I can fix the stereo > clashes?
Most likely this is due to a poor alignment. But you would need to look at the clashes in a PDB viewer to see what's going on.
Ben Webb, Modeller Caretaker
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Li,Haoxi -
Modeller Caretaker