Hello All, I have the following problem. Whenever I attempt to load a pdb file from the RCSB (eg- a .ent file), I get the following error.
ObjectMolecule: read HELIX A 231 A 241 ObjectMolecule: read HELIX A 265 A 286 ObjectMolecule: read HELIX A 293 A 317 ObjectMolecule: read HELIX A 334 A 339 ObjectMolecule: read HELIX A 344 A 353 ObjectMolecule: read HELIX A 353 A 360 ObjectMolecule: read HELIX A 363 A 376 ObjectMolecule: read HELIX A 385 A 408 Bus error ...and Pymol crashes. This happens on every .ent file I have downloaded, and I have traced the problem to something with the secondary structure assignments. When I delete them from the file, it loads fine. The format of the lines is (spacing is different since I'm not in courier text mode): HELIX 1 1 PRO A 231 ALA A 241 1 11 HELIX 2 2 VAL A 265 ILE A 286 1 22 HELIX 3 3 PRO A 293 SER A 317 1 25 HELIX 4 4 ARG A 334 SER A 339 1 6 HELIX 5 5 ALA A 344 LEU A 353 1 10 HELIX 6 6 LEU A 353 MET A 360 1 8 HELIX 7 7 ASP A 363 PHE A 376 1 14 HELIX 8 8 ASN A 385 TYR A 408 1 24 HELIX 9 9 GLY A 413 LEU A 420 1 8 HELIX 10 10 ARG A 421 LEU A 441 1 21 HELIX 11 11 PHE A 450 LEU A 455 1 6 HELIX 12 12 GLU D 207 PHE D 226 1 20 HELIX 13 13 THR D 229 GLY D 239 1 11 HELIX 14 14 ASP D 251 ASP D 260 1 10 HELIX 15 15 ASP D 260 LYS D 265 1 6 HELIX 16 16 GLU D 276 SER D 302 1 ...etc... Any ideas? I would hate to have to manually assign the secondary structure elements for every pdb file in the RCSB! Also, I'm using Pymol 0.68 (I've downloaded the binaries for 0.78 but haven't unpacked them). Felix Felix F. Vajdos Pfizer Inc Eastern Point Road MS 4039 Groton, CT 06340 860-715-6504 LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.
