<HTML>
<HEAD>
<TITLE>Ligandfit bug report</TITLE>
</HEAD>
<BODY>
<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>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:<BR>
</SPAN></FONT><SPAN STYLE='font-size:11pt'><FONT FACE="Courier, Courier New">HETATM 17 C16 LIG 1 -83.510 -0.856 0.582 1.00 20.00 C <BR>
HETATM 18 O01 LIG 1 -86.640 -2.401 -0.357 1.00 20.00 O <BR>
HETATM 19 O LIG 1 -75.199 2.925 2.145 1.00 20.00 O <BR>
HETATM 20 C17 LIG 1 -83.058 -0.188 1.872 1.00 20.00 C <BR>
HETATM 21 C LIG 1 -76.676 0.780 -1.835 1.00 20.00 C <BR>
<BR>
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. <BR>
<BR>
Best, <BR>
Kendall Nettles<BR>
</FONT></SPAN>
</BODY>
</HTML>