Hi Ramon, * Ramon Crehuet <rcs...@iiqab.csic.es> [2005-07-29 12:55] wrote: > 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?
The problem is that the two states have different chain identifierss. They must be the same for intra_fit to work. Here are your two example pdb files that do work now. CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ATOM 1 N GLY A 5 45.046 30.918 26.469 1.00 13.37 2CHT ATOM 2 CA GLY A 5 45.321 29.775 27.300 1.00 8.71 2CHT ATOM 3 C GLY A 5 45.834 28.644 26.444 1.00 4.68 2CHT ATOM 4 O GLY A 5 45.402 28.423 25.303 1.00 3.21 2CHT ATOM 5 N ILE A 6 46.763 27.874 26.979 1.00 5.74 2CHT ATOM 6 CA ILE A 6 47.318 26.743 26.260 1.00 3.53 2CHT ATOM 7 CB ILE A 6 48.842 26.828 26.098 1.00 4.24 2CHT ATOM 8 CG1 ILE A 6 49.254 28.223 25.623 1.00 4.37 2CHT ATOM 9 CG2 ILE A 6 49.258 25.732 25.115 1.00 2.06 2CHT ATOM 10 CD1 ILE A 6 50.724 28.468 25.301 1.00 6.67 2CHT ATOM 11 C ILE A 6 46.981 25.563 27.127 1.00 4.66 2CHT ATOM 12 O ILE A 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 Cheers, Rob -- Robert L. Campbell, Ph.D. <r...@post.queensu.ca> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
