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Hi Chris-- > > I ran the program with the -quick flag. So I only expected to see the > first 36 residues. I also checked the disk quota and there is plenty of > disk space so that shouldn't be a problem. I made a truncated version of > the cvn_reference.pdb ending at LEU 36 O. Then I modified refine.py line > 84 to load the truncated file. Now it tells me the selections are of > unequal length, in regards to non-H atoms (See output below). Both files > contain 518 atoms at the terminal O, so without looking over each atom I > would assume the number of non-H atoms is the same. > > Thanks, > CDW > > loading pdb file: ./cvn_reference_trunc.pdb?? [psf]PDBTool:read: atom > not found in structure:? LEU 36 O > > ?matchInexactAtomEntry: matching entry??????? 36 O to atom? 36 > OT1 > initCoords: still 3 unknown atomic coordinates > ?[coords] > cmpSel: selections are of unequal length: > ? 0: not name H* -- 265 atoms > ? 1: not name H* -- 266 atoms > still some slight difference with the heavy atoms in the terminal residue. It's easiest to just drop the cmpSel argument to create_PosDiffPot. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkowB/wACgkQPK2zrJwS/lb9KgCfV+EwsKnyprkQ4vWUR4VZdipQ 0T4An2FehhPc+a1A4rugeDQroTxCG22I =bBXe -----END PGP SIGNATURE-----
