So I have a molecule (a dsRNA) , that has two conformations. I want to align it in pymol with molecules but I get the following error: ExecutiveAlign error: atomic alignment failed (mismatched identifiers? )
So I try removing the conformations and maintain the spaces also, however no luck. INfact after editing and displaying the sequence in pymol, the chain ids seem to get interleaved as follows:
I am writing here sample text from the molecule that has both the conformations:
ATOM 1 O3'A C C 1 -7.005 37.688 50.581 0.60 29.09 O
ATOM 2 O3'B C C 1 -6.653 36.261 51.094 0.40 28.26 O
ATOM 3 P A C C 1 -8.284 38.506 50.584 0.60 27.34 P
ATOM 4 P B C C 1 -8.150 36.411 51.318 0.40 28.35 P
ATOM 5 O1PA C C 1 -8.747 38.916 51.969 0.60 27.60 O
ATOM 6 O1PB C C 1 -8.852 35.063 51.303 0.40 26.74 O
and the molecule after removing the conformers, editing the identifier number, and maintaining the spaces as found in usual PDB files:
From chain C:
ATOM 1 O3' C C 1 -7.005 37.688 50.581 0.60 29.09 O
ATOM 2 P C C 1 -8.284 38.506 50.584 0.60 27.34 P
ATOM 3 O1P C C 1 -8.747 38.916 51.969 0.60 27.60 O
ATOM 4 O2P C C 1 -8.241 39.648 49.584 0.60 28.40 O
ATOM 5 O5' C C 1 -9.442 37.507 50.040 0.60 28.29 O
From chain D:
TER 446 U C 21
ATOM 447 O3' C D 1 -11.398 37.360 86.614 0.60 24.03 O
ATOM 448 P C D 1 -11.903 36.706 87.889 0.60 26.14 P
ATOM 449 O1P C D 1 -12.702 37.680 88.743 0.60 28.36 O
Please help, at the end of the day I would like to align this molecule with other molecules in pymol without getting the error. Thanks
