Upon discussions with some of my colleagues, we're guessing you didn't even use an alignment file -- you just associated the structure with the target sequence directly and then ran Modeller. That doesn't work if the target sequence has a deletion relative to the template sequence. So until we fix that just use the alignment file I sent. --Eric
On Nov 28, 2023, at 10:49 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Zoey, The alignment you use has to have the actual sequence of the template structure. In your alignment file, the four characters starting at position 81 of the template sequence are KMPK, whereas the corresponding part of the actual template structure is KMMSPK. If I insert the missing "MS" into the template sequence and corresponding gap characters in the target sequence, then Modeller works. I will send an edited alignment file with those changes in a separate email.
--Eric
Eric Pettersen UCSF Computer Graphics Lab