I've been trying to do insert a pose (which is a part of a pdb file) into a new pose ('pose'), which was made from sequence (it's just 40 x 'A'). To get the fragment I want from the pdb pose, I used return_region:
region = return_region(sheet1,12,length1+12)
(sheet1 was the pdb file pose, length1 was specified before).
Then, I tried:
and while I didn't get an error, the pose was appended by a jump, and I wanted it to be by peptide bond;
So, I tried to go with:
mover = AnchoredGraftMover(2, length1+1, region)
But it resulted with 'segmentation fault (core dumped). CCDEndsGraftMover didn't work either: 'Graft meets ideal geometry false' (the "peptide bond" was ~ 37 instead of 1.5).
ft = FoldTree()
ft.add_edge(length1+2, pose.total_residue(), -1)
ft2 = FoldTree()
new = insert_pose_to_pose(pose,region,2,length1+2)
I got: "segmentation fault (core dumped)" - I assume it may be because my foldtree isn't good, though I don't fully understand how to correct it?
Or maybe my poses need some preparation?
Since I want to insert the region in the beginning of the pose made from sequence, I thought of just appening it with residues (and I just wanted to test if this would work),
but it resulted with an error message: can't create a polymer bond to new residue 23 due to incompatible type: ALA : NtermProteinFull
I also tried simply copying phi and psi of residues from region to my pose, but the result didn't look the same, even with omega copied as well.
Am I going about this the wrong way? Thank you so much for any response.