Blind almost always mean something is there. But your resolution is low. Scaling procedures st that resolution can cause misleading features to appear.
Q1. How good is your Wilson plot? If you used the ccp4 data scaling etc it will have given you plots and comments. If you send s log file that would help. Q2. You presumably know what you crystallised. Are there any missing bits , ligands to put in those blobs? Q3. Look at the bfactor analysis. Are any parts spectacularly high which would suggest those are wrong and should be deleted then rebuilt? But 3.2 A maps are a pain Good luck Eleanor To test scaling On Thu, 1 Apr 2021 at 07:29, Paul Emsley <[email protected]> wrote: > On Wed, 2021-03-31 at 19:48 -0400, Jessica Besaw wrote: > > > > I once again am asking for your advice. ☺ I am trying to solve the > > structure of an RBD:Fab complex. > > > > After molecular replacement, the density fits the model very well. > > Looking at the overall crystal structure (by applying symmetry mates > > in pymol), I see large pores in the crystal with only little bits of > > density as shown in the figure below. > > > > After doing refinement in phenix.refine, I now get these HUGE blobs > > of density. But, they don't really interact with any part of the > > structure, mostly just "floating" in the center, as shown in the > > figure below. I have attached my current refinement strategy in case > > I am choosing a poor strategy. > > > > Question: > > (1) Are these blobs likely to be a protein? > > (2) If it is not a protein, is there an honest / scientifically- > > approved way to deal with these density blobs. I think they are > > keeping my R values very high. > > > > Potentially useful information: > > Rwork/Rfree = 27.1 / 30.1 > > Spacegroup: P 32 2 1 > > Highest Resolution: 3.35 Angstrom > > Completeness: 99% (99%) > > CC1/2: 0.99 (0.35) > > > > I imagine that the bulk solvent model/structure factor > calculation/scaling is different between the first image and the > second. Try blurring the first set of SFs by 90 A^2 or so and see if > the blobs turn up to some extent. It does *seem* as if there is some > connection to your model at about the 5 o'clock position of the left > circle. > > This being CCP4BB, it is not inappropriate to suggest that you try > another refinement program, one which has a different bulk solvent > model (or a number of them from which to choose, even) to see if your > blobs are recapitulated. > > So my answers to your questions are currently > (1) I don't know, it's a close call > (2) put atoms in them > > Paul. > > I always like "what's my blob?" questions. > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
