Ngan You can very easily access the files in the chemical components that are installed with PHENIX using phenix.elbow --chemical_components=CR2 or to view the ligand phenix.reel --chemical-components cr2 (case is unimportant) You can also get the Mogul values (if you have Mogul installed and in you $PATH and a recent PHENIX version) phenix.elbow --chem=cr2 --mogul Using the chemical components input in the latest eLBOW release, I tabulated the bond lengths for C3-CA3 in CR2 eLBOW : 1.492 AM1 : 1.567 Mogul GUI: 1.528 with a range up to 1.56 Mogul command-line : 1.511 I'm sure you will agree that not every C-C bond should be 1.51A. There is a range so any attempt to construct a ligand with exactly 1.51A for all C-C bonds is wrong. The range in Mogul is about 0.02 Angstrom. There are of course limits to the accuracy of any method used to determine a bond length but I believe that eLBOW and AM1 gets within the acceptable range for most ligands. Some of the other problems you are seeing may be due to using a PDB file as input. Its always better to use the --chemical-components or some other chemically rich format. Nigel On Wed, Apr 20, 2011 at 3:23 AM, Ngan Nguyen Bich wrote:

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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709     Email : [email protected] Fax   : 510-486-5909       Web  : CCI.LBL.gov