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
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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