Hi Ian, It's easy to forget about LINK records and such when dealing with the coordinates (I recently had to fix a bug in my own code for that). The problem with insertion codes is that they are very poorly defined in the PDB standard. Does 128A come before or after 128? There is no strict rule for that, instead they are used in order of appearance. This makes it hard for programmers to stick to agreed standards. Instead people rather ignore insertion codes altogether. They are really poorly soppurted by many programs. Perhaps switching to mmCIF gets rid of the problem.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Ian Tickle > Sent: Wednesday, December 05, 2012 16:39 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] thanks god for pdbset > > The last time I tried the pdbset renumber command because of issues with > insertion codes in certain programs, it failed to also renumber the LINK, > SSBOND & CISPEP records. Needless to say, thanking god (or even God) was > not my first thought! (more along the lines of "why can't software > developers stick to the agreed standards?"). > > I haven't tried it with the latest version, maybe it's fixed now. > > -- Ian > > > > On 5 December 2012 07:58, Francois Berenger <beren...@riken.jp> wrote: > > > Especially the renumber command that changes > residue insertion codes into an increment of > the impacted residue numbers. > > Regards, > F. > >
