CCP4 has a number of such utilities, such as pdbset. http://www.ccp4.ac.uk/html/pdbset.html
You can find others by looking here: http://www.ccp4.ac.uk/html/FUNCTION.html HTH, William G. Scott http://scottlab.ucsc.edu/~wgscott On Oct 7, 2014, at 11:01 AM, Sasha Pausch <sashapau...@gmail.com> wrote: > Thank you Scott, I could change the nomenclature. But is there any way to > change the numbering also? > My PDB is not being accepted by NUCPLOT. Initially I suspected it is the > nomenclature, even after changing nomenclature as per your suggestion program > is not accepting the PDB. Now I am suspecting is the numbering of the bases > different!! > > Please help on overcoming this problem. > > > On Tue, Oct 7, 2014 at 12:58 AM, William G. Scott <wgsc...@ucsc.edu> wrote: > > > > > On Oct 6, 2014, at 12:04 PM, Sasha Pausch <sashapau...@gmail.com> wrote: > > > > Hello All, > > > > I would like to know how to change the nomenclature of bases (for example > > from Ad to DA for adenosine triphosphate) in PDB file. > > perl -pi -e ‘s|Ad|DA|g’ your.pdb > > >
