I hope that some [X]Emacs expert can rewrite Charlie Bond's wonderful pdb-mode to work with mmCIF files (or at least the coordinate bits)
… for exactly the reasons Phil Jeffrey points out Phil On 8 Aug 2013, at 00:54, "Jeffrey, Philip D." <pjeff...@princeton.edu> wrote: > Nat Echols wrote: > > Personally, if I need to change a chain ID, I can use Coot or pdbset or > > many other tools. Writing code for > > this should only be necessary if you're processing large numbers of models, > > or have a spectacularly > > misformatted PDB file. > > Problem. Coot is bad at the chain label aspect. > Create a pdb file containing residues A1-A20 and X101-X120 - non-overlapping > numbering. > Try to change the chain label of X to A. > I get "WARNING:: CONFLICT: chain id already exists in this molecule" > > This is (IMHO) a bizarre feature because this is exactly the sort of thing > you do when building structures. > > Therefore I do one of two things: > 1. Open it in (x)emacs, replace " X " with " A " and Bob's your uncle. > 2. Start Peek2 - that's my interactive program for doing simple and stupid > things like this. I type "read test.pdb" and "chain" and Peek2 prompts me at > perceived chain breaks (change in chain label, CA-CA breaks, ATOM/HETATM > transitions &c) and then "write test.pdb". Takes less than 10 seconds. > CCP4i would probably still be launching, as would Phenix. > > The reason I do #1 or #2 is not to be a Luddite, but to do something trivial > and boring quickly so I can get back to something interesting like building > structures, or beating subjects to death on CCP4bb. > > What's lacking is an interactive, or just plain fast method in any guise, way > of doing simple PDB manipulations that we do tons of times when building > protein structures. I've used Peek2 thousands of times for this purpose, > which is the only reason it still exists because it's a fairly stupid > program. A truly interactive version of PDBSET would be splendid. But, > again, it always runs in batch mode. > > mmCIF looked promising, apropos emacs, when I looked at the spec page at: > http://www.iucr.org/__data/iucr/cifdic_html/2/cif_mm.dic/Catom_site.html > because that ATOM data is column-formatted. Cool. However looking at > 6LYZ.cif from RCSB's site revealed that the XYZ's were LEFT-justified: > http://www.rcsb.org/pdb/files/6LYZ.cif > which makes me recoil in horror and resolve to use PDB format until someone > puts a gun to my head. > > Really, guys, if you can put multiple successive spaces to the RIGHT of the > number, why didn't you put them to the LEFT of it instead ? Same parsing, > better readability. > > Phil Jeffrey > Princeton > (using the vernacular but deathly serious about protein structure)
