There is a CCP4 program that deals with PDB files, I can't remember the name though (there are so many programs within CCP4...). It will "standardize" your PDB file. The program might be called pdbcur or pdbset , I am not certain... So I would either try pdbcur and pdbset, or send an email to ccp4bb to inquire there. Fred. Oliver King wrote:
Hi Fred,
Thanks for the helpful suggestion, however it isn't just Leu residues it's Val, Ile, Ala, Pro and others that suffer this problem. I just tried to regularise the Leu and then refine again in Phenix and now both the CD1 and CD2 atoms have detached! ATOM 1 N LEU A 8 50.623 -35.571 -6.058 1.00 52.51 N ATOM 2 CA LEU A 8 49.795 -35.076 -4.891 1.00 52.71 C ATOM 3 CB LEU A 8 50.211 -33.647 -4.508 1.00 49.42 C ATOM 4 CG LEU A 8 51.469 -33.402 -3.616 1.00 57.61 C ATOM 5 CD1 LEU A 8 51.910 -31.789 -3.631 1.00 55.67 C ATOM 6 CD2 LEU A 8 51.323 -34.077 -2.105 1.00 53.78 C ATOM 7 C LEU A 8 48.247 -35.000 -5.245 1.00 48.34 C ATOM 8 O LEU A 8 47.949 -34.270 -6.261 1.00 47.33 O
Initially I thought that my monomer library was corrupt, however the same happens both after reinstalling Phenix and when refining on a different installation on another computer. I was just hoping to find a way to standardise the PDB file format between the two programs but realise that this may open a whole can of worms!
Thanks,
Olly