Dear Phenix developers, I'm quite new in crystallography and use PhenixGUI for refinement my protein. I got a problem when I had to create cif file of the new ligand to feed in phenix_refine by Elbow/ReadySet I saw that program creates some bonds shorter or longer compared to the statistic value from the CSD for example. Here are some examples when I play with Elbow (same problem with ReadySet) 1. when I feed program the chemical string, (template PDB file is the mylidand_idea.pdb) CR2 C3 CA3 single 1.569 0.038 and if I choose AM1 optimization CR2 C3 CA3 single 1.602 0.040 2. when I feed program the .pdb file, choose Use geometry for Initial geometry. GYC N CA1 single 1.409 0.020 * GYC N HN1 single 0.902 0.020 GYC N HN2 single 0.901 0.020 GYC SG1 CB1 single 1.797 0.020 GYC SG1 HG1 single 1.204 0.020 GYC CB1 CA1 single 1.500 0.020 GYC CB1 HB11 single 1.006 0.020 GYC CB1 HB12 single 0.972 0.020 GYC CA1 C1 single 1.528 0.020 GYC CA1 HA1 single 1.010 0.020 GYC C1 N2 aromatic 1.412 0.020 GYC C1 N3 aromatic 1.304 0.020 GYC N2 CA2 aromatic 1.505 0.020 ** GYC N3 C2 aromatic 1.349 0.020 GYC N3 CA3 single 1.423 0.020 GYC C2 O2 double 1.370 0.020 GYC C2 CA2 aromatic 1.509 0.020 GYC CA2 CB2 single 1.532 0.020 GYC CA3 C single 1.496 0.020 It's strange to me when comparing * and ** and if I run AM1 GYC CB1 CA1 single 1.533 0.035 GYC CA3 C single 1.564 0.035 as I know, the C-C single bond should be about 1.51. Does anyone get a problem like me? I wonder if I didn't do properly or some thing else, or any suggestion for my case. One more questions is that afterward I found cif file (seemly mmcif file) of my ligand in phenix-1.7-650/chem_data/chemical_components And I'm wondering that How the program use these cif file, or I can use them in which way? Thank you in advance. Best regards, Ngan Nguyen Bich KULeuven Belgium