Dear all, thank you very much for all your suggestions. The one that worked for me was Sam's actually. Indeed in that column I had As, then nothing, then also Ds, and Vs or some other letters... I don't know. I just removed the whole column and now when I open it in pymol it looks good!
Super thanks!! Best, Almu 2015-02-05 18:33 GMT+01:00 Horrell, Sam <sam.horr...@liverpool.ac.uk>: > 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 > > -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
