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)