Kendall Please send all the files directly (not the list). I believe your first problem has been fixed recently but the second is strange. Cheers Nigel On Mon, Jan 24, 2011 at 1:46 PM, Kendall Nettles wrote:

We are generating pdb files with chemdraw3D, which turn out to not be “real” pdb files. PHENIX.ELBOW fixes them, but leaves some of the atom ID numbers blank, such as Oxygen #2, and Carbon #18: HETATM   17  C16 LIG     1     -83.510  -0.856   0.582  1.00 20.00           C HETATM   18  O01 LIG     1     -86.640  -2.401  -0.357  1.00 20.00           O HETATM   19  O   LIG     1     -75.199   2.925   2.145  1.00 20.00           O HETATM   20  C17 LIG     1     -83.058  -0.188   1.872  1.00 20.00           C HETATM   21  C   LIG     1     -76.676   0.780  -1.835  1.00 20.00           C

After editing it to add in the missing numbers, I re-ran elbow, and found that the resulting optimized ligand had imploded, producing altered atom connectivity. If I ran it with --final_geometry it came out OK. If you would like files to reproduce the error, I am happy to send them.

Best, Kendall Nettles

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