-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Dialing,
it can easily happen to have some electron density one cannot explain, as a combination of disorder, noise, and maybe chemicals present in the crystals you are not aware of. In such a case you build the model as well as you can, leaving a remark in the PDB file and the publication about the left-over density. In your case, however, the area B might become clearer after you build the four lysines at A, and it might resolve to something interpretable. Cheers, Tim On 12/14/2011 03:10 AM, Dialing Pretty wrote: > > > > Dear Paul, > > Attached are 2 images (same coot blob electron density map from 2 > different views) for my blob electron density map. > > In the left part, I labeled 4 "K", indicating 4 lysine side chains, > and it corresponds to my peptide sequence. However at the end of the > last K (right tip of the left part blob electron density map), there > should be another 2 residues (here I call 2 extra residues). The > first explanation is that the 2 extra residues are disordered, and > therefore no electronic density for them. > > The second explanation is that the whole blob electron density map is > discontinuous, and correspondingly I labeled the right part of it as > "B", and it could be that the part of electron density labeled "B" > corresponds to of the 2 extra residues. However in this way there is > no electron density in B part corresponds to the side chain of the > extra residue (1 extra residue with rather larger side chain), what > is more the distance between the last "K" and any of the 2 extra > residues would be far more than a single normal baton distance. > > But if we do not explain the part labeled "B" as the electronic > density as for "2 extra residues", the part of electron density > labeled "B" would be too large to be explained by ions. > > I am looking forward to getting a reply from you how you process it > if you meet this situation. > > Cheers, > > Dialing - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO6GxPUxlJ7aRr7hoRAgGeAKCQ7SWT4Odq6EUIKdG8wqWZvCgn2QCePkWd FzXlLX0g8QGB1m+pTvSLIrY= =uicf -----END PGP SIGNATURE-----
