Hi all,
I have a problem with intra_fit. After reading two (or more) pdb
into the same molecule, it does not recognise atoms for other states. I
always get the message (this is for a short example):
PyMOL>intra_fit name ca, 1
Executive-Warning: Missing atoms in state 2 (0 instead of 2).
Executive-Warning: No matches found for state 2.
even after executing:
PyMOL>alter all, chain =''
Alter: modified 24 atoms.
How can I know what is different in the two states or why the selection
doesn't work?
Thanks,
Ramon
I enclose two pdb files as examples that do not work.
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ATOM 1 N GLY B 5 45.046 30.918 26.469 1.00 13.37 2CHT
ATOM 2 CA GLY B 5 45.321 29.775 27.300 1.00 8.71 2CHT
ATOM 3 C GLY B 5 45.834 28.644 26.444 1.00 4.68 2CHT
ATOM 4 O GLY B 5 45.402 28.423 25.303 1.00 3.21 2CHT
ATOM 5 N ILE B 6 46.763 27.874 26.979 1.00 5.74 2CHT
ATOM 6 CA ILE B 6 47.318 26.743 26.260 1.00 3.53 2CHT
ATOM 7 CB ILE B 6 48.842 26.828 26.098 1.00 4.24 2CHT
ATOM 8 CG1 ILE B 6 49.254 28.223 25.623 1.00 4.37 2CHT
ATOM 9 CG2 ILE B 6 49.258 25.732 25.115 1.00 2.06 2CHT
ATOM 10 CD1 ILE B 6 50.724 28.468 25.301 1.00 6.67 2CHT
ATOM 11 C ILE B 6 46.981 25.563 27.127 1.00 4.66 2CHT
ATOM 12 O ILE B 6 47.066 25.628 28.361 1.00 9.30 2CHT
END
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ATOM 1 N GLY A 5 45.044 31.002 26.859 1.00 7.52 2CHT
ATOM 2 CA GLY A 5 45.492 29.807 27.582 1.00 2.01 2CHT
ATOM 3 C GLY A 5 45.989 28.671 26.692 1.00 3.74 2CHT
ATOM 4 O GLY A 5 45.500 28.434 25.576 1.00 2.36 2CHT
ATOM 5 N ILE A 6 46.957 27.882 27.123 1.00 6.04 2CHT
ATOM 6 CA ILE A 6 47.441 26.744 26.357 1.00 13.49 2CHT
ATOM 7 CB ILE A 6 48.955 26.937 25.996 1.00 14.13 2CHT
ATOM 8 CG1 ILE A 6 49.190 28.322 25.354 1.00 19.71 2CHT
ATOM 9 CG2 ILE A 6 49.359 25.924 24.936 1.00 12.19 2CHT
ATOM 10 CD1 ILE A 6 50.665 28.738 25.151 1.00 20.45 2CHT
ATOM 11 C ILE A 6 47.222 25.473 27.194 1.00 13.81 2CHT
ATOM 12 O ILE A 6 47.782 25.283 28.269 1.00 13.60 2CHT
END
