Dear Artem, Thank you for your help. And I will use the hyperlink option next time.
Cheers On May 7, 2015 10:08 PM, "Artem Evdokimov" <[email protected]> wrote: > 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* >> > >
