Down load the MOGUL coordinates and use some program - PRODRG LIBCHECK ELBOW to make a new dictionary.. Then check it! You can assign that dictionary as LIBIN and the new ATP will have precedence over the wrong one. Eleanor
On 27 August 2014 18:25, Matthias Zebisch < [email protected]> wrote: > Cant you edit the ATP.cif on your computer to have the correct expected > bond length? > > Best, Matthias > > ----------------------------------------- > Dr. Matthias Zebisch > Division of Structural Biology, > Wellcome Trust Centre for Human Genetics, > University of Oxford, > Roosevelt Drive, > Oxford OX3 7BN, UK > > Phone (+44) 1865 287549; > Fax (+44) 1865 287547 > Email [email protected] > Website http://www.strubi.ox.ac.uk > ----------------------------------------- > > On 8/27/2014 4:12 PM, Bernard D Santarsiero wrote: > > I recently refined a structure in CCP4/REFMAC with ATP in the structure. > Upon submission to Acta for publication, the wwPDB validation report was > run. Several things were flagged, including the C4-C5 bond in the adenosine > moiety as being too long. It generally refines to 1.46-1.47A. The "ideal" > distance in the validation report is 1.38A, and the upon review of the > ATP.cif file in the REFMAC library, the target distance is 1.49A (and > listed as a double bond). Clearly 1.37-1.38A is a reasonable target value. > HIC-Up gives the target bond length as 1.404A. > > Where can I grab a revised ATP.cif file? I guess I'll need to re-refine > all of my structures and re-run the validation report. > > BTW, I also looked at the PDB_REDO structure report for my structure, > and can't reproduce the Rcryst and Rfree values with the same model. > > Bernie > -- > Bernard D. Santarsiero > Research Professor > Center for Pharmaceutical Biotechnology and the > Department of Medicinal Chemistry and Pharmacognosy > Center for Structural Biology > Center for Clinical and Translational Science > University of Illinois at Chicago > MC870 3070MBRB 900 South Ashland Avenue > Chicago, IL 60607-7173 USA > (312) 413-0339 (office) > (312) 413-9303 (FAX) > http://www.uic.edu/labs/bds > http://scholar.google.com/citations?user=fGauLBMAAAAJ > > >
