[phenixbb] Ligandfit bug report

Kendall Nettles knettles at scripps.edu
Mon Jan 24 13:46:54 PST 2011


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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