Hi Almudena, Have a look in your PDB file in the second to last colum, if it looks something like the example below then delete the As from the fine and it should connect up. I've had this before, not sure where it came from but removing it fixed the problem.
ATOM 371 CA PRO A 48 -11.300 -19.315 -35.308 1.00 91.62 C ATOM 372 CB PRO A 48 -10.546 -20.584 -35.726 1.00 90.06 C ATOM 373 CG PRO A 48 -9.106 -20.254 -35.548 1.00 91.26 C ATOM 374 CD PRO A 48 -8.992 -19.119 -34.570 1.00 91.06 C ATOM 375 C PRO A 48 -12.669 -19.668 -34.722 1.00 85.38 C ATOM 376 O PRO A 48 -13.686 -19.209 -35.228 1.00 79.05 O ATOM 377 N ARG A 49 -12.683 -20.461 -33.658 1.00 91.80 A N ATOM 378 CA ARG A 49 -13.936 -20.872 -33.022 1.00101.75 A C ATOM 379 CB ARG A 49 -13.717 -22.064 -32.077 1.00109.37 A C ATOM 380 CG ARG A 49 -15.008 -22.749 -31.637 1.00106.33 A C ATOM 381 CD ARG A 49 -14.933 -23.259 -30.207 1.00104.16 A C Hope that helps, Sam ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Almudena Ponce Salvatierra [maps.fa...@gmail.com] Sent: 04 February 2015 17:07 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off topic pymol Dear all, does anyone know why if I open a pdb in pymol (that appears normal and fully connected in coot) it appears as if it was broken into pieces? Thanks, Almudena. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
