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 [[log in to unmask]] on behalf of Almudena Ponce Salvatierra [[log in to unmask]]
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 <[log in to unmask]<mailto:[log in to unmask]>>:
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 [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Almudena Ponce Salvatierra [[log in to unmask]<mailto:[log in to unmask]>]
Sent: 04 February 2015 17:07
To: [log in to unmask]<mailto:[log in to unmask]>
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
--
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