Two topics today... 1) Problem with LIBCHECK.
Thanks to all who replied to my issue. I was able to resolve the issue before the flurry of responses came in. Basically, I took my CSA modified amino acid, aligned it as best I could to the CYS (especially at the CA), and then manually edited the PDB file to include the new CSA atoms from CB onward, leaving the backbone as the CYS atoms, and changing all the residue names to CSA. Of course, this meant that the CSA sidechain was in no-man's land, but anyway, refined it in PHENIX restraining the distance from the terminal carbon and the sulfur of the crosslink partner to 1.83 +/- 0.05 A, and let 'er rip, including the .cif file for CSA in the monomer library in my .def file. The output was good enough to refine manually, and I'm happy with the results. 2) re: problems in refinement Petr, I second Pavel's recommendations. Furthermore, in your second case with the positive difference density for residues that seem to be refined well, I had something like this happen for me, although at much lower (3.1 A) resolution. I fixed it by making those trouble residues a TLS group and refining with TLS in PHENIX. After one round of refinement, the problem was fixed and I was able to remove TLS from the refinement strategy. Hope it helps, Geoff -- Geoffrey K. Feld Department of Chemistry 492 Stanley Hall University of California, Berkeley "Vigilia pretium libertatis"
