Dear Almudena,
Those letter represents different peptide chains. I guess in your cases they were probably peptide fragments built by automatic building programs such as arp/warp or buccaneer. Some programs do create PDB files with that extra column, which seems to send Pymol a bit awry. Best, D ________________________________ From: CCP4 bulletin board [[email protected]] on behalf of Almudena Ponce Salvatierra [[email protected]] Sent: 12 February 2015 15:30 To: ccp4bb Subject: Re: [ccp4bb] off topic pymol 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 <[email protected]<mailto:[email protected]>>: 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 [[email protected]<mailto:[email protected]>] on behalf of Almudena Ponce Salvatierra [[email protected]<mailto:[email protected]>] Sent: 04 February 2015 17:07 To: [email protected]<mailto:[email protected]> 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 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
