Blobs 3, 5, and 7 are likely poorly modeled or alternative sidechains. The rest - hard to say from static imagery.
Artem P.S. the etiquette of the board is that large attachments are not nice to people who read stuff on portable devices or over slow connections. It is considerably nicer to use hyperlinked free image hosting options, instead. - Cosmic Cats approve of this message On Thu, May 7, 2015 at 10:00 AM, Mohd Syed Ahangar <[email protected]> wrote: > Dear all, > > I am on the final stages of refining my structure. It is a 2.1 a data > and the Rwork and Rfree currently are 23.75 and 27.23. I am trying to > now figure out some blobs for which I need help. I have attached the > pictures of 6 blobs (sorry, the pictures are numbered till 7, with 5 > missing). Can anyone help me fihure out what could fit in these blobs? > The crystallization condition and protein buffer contained HEPES, > NaCl, PEG 2,000 and sodium acetate. > > The specific description of each blob is: > Blob-1: I am confused about the four blobs showing up > Blob-2: There are similar blobs at many other places. It doesnt show > any Fo-Fc density, but lies in between two residues > Blob-3: There is one such blob in all the three chains of the molecule > Blob-4: I have tried flipping the neighbouring residues, but it doesnt > help. > Blob-6: The main chain amino groups already show good fitting into the > density. So, what could be this blob in the main chain? Similar blobs > are also present at other places. > Blob-7: I tried fitting an alternate confirmation of Arginine, but > that didnt work either. > > Moreover, how do I get rid of lone positive and negative densities in > the difference map with no corresponding density in the Fo-Fc map? > > Also, are the default values in coot validation used for finding > difference peaks (sigma cutoff 5) and analyzing waters (B-factor: 80 > and sigma cut off less than 1) good enough? Or what other values can I > play around with? > > I know the queries are many, but hope to get some useful tips. > > Thanks in advance > > -- > > > *A.M.Saeed* >
