Thank you, everyone! 1. Paul advised me to use:
tr '\015' '\012' < ligand-from-prodrg.cif > fixed.cif Reads into coot just fine. 2. Nigel Moriarty advised: phenix.elbow --smiles "smiles string" --reel --opt Stopping just after the smiles string works too, but --opt takes longer but results in better geometry. Thank you, once again! Sangeetha. On Wed, Mar 18, 2009 at 2:39 PM, Paul Emsley <[email protected]>wrote: > Sangeetha Vedula wrote: > >> I get the dirty mmcif message in the terminal window. >> >> This is the message I get: >> >> dirty mmCIF file? /Users/......./r-pento.cif >> Bad CIFRC_Ok on ReadMMCIFFile >> init_refmac_mon_lib /Users/......./r-pento.cif had no bond restraints >> >> > For the record, > > It turns out that this was a DOS->Unix conversion issue. > I am reminded to make the error output more verbose than simply "dirty > cif". I've made a note. > > Thanks, > > Paul. >
