The comments on overloads are interesting and can be checked on your raw images by zooming in to suspected overload reflections.
Do the maps look good. What is Rfree. When you try anisotropic refinement what does Rfree do. Have you put Hydrogen atoms as riders? Questions not answers, sorry James Phillips Retired, but busy On Thu, Oct 11, 2018 at 03:46 Tim Gruene <tim.gru...@psi.ch> wrote: > Dear Guto, > > integration programs often ignore overloads, and most of them know the > detector cut-offs. mosflm has the option to estimate the resolution of > overloaded reflections from the none-overloaded parts. This should not > be a replacement for proper collection of a low resolution data set, but > it may help you identify the source of problems. > > You might also want to check your low resolution cut-off. Maybe you have > a few strong reflections that are shaded by the beam stop. If these were > integrated, and a symmetry equivalent reflection was not shaded, it will > result in a large discrepancy between those two reflections. If it is a > strong reflection, it may ruin your low resolution statistics: aimless > lists only 88 reflections in the low resolution shell. > > You mentioned that the difference map does not indicate unmodelled parts > of the molecule. You may still have those, and if they cannot be > modelled, they may affect your model R values. > > In case you are unsure about the space group, you could try solving the > structure with SHELXT. I have done this with a unit cell volume about > twice as big as your. Those data reflected to 0.7A resolution (which > could make a very big difference), but the data quality was quite poor > (because of a large number of overloads). SHELXT would try to find the > best matching space group within the Laue group, and you can test > several Laue groups. In my case, it took SHELXT about 10min (790s) to > solve the structure in P212121. Since you have only about 1A resolution, > you could increase the number of trials with the option '-m500'. > > Best, > Tim > > On 10/11/2018 10:13 AM, Guto Rhys wrote: > > Hi all, > > > > Firstly, I’d like to say I’m really impressed with the volume, speed and > detail of the response that I have received. Thanks everyone. > > > > Overloads > > Eddie, Marc, Eleanor, Harry and Misha; thanks to all for suggesting > collection strategies and identifying the likely issue. Yesterday, I had a > quick look at the images and the lower-resolution reflections do look > overexposed. Thanks for the offer to check the images Graeme. > > > > Weightings and anisotropic refinement > > Wim, Matthias and Robbie; sorry I had forgotten to mention that I ran > the structure through pdbredo to optimise weights and already refined using > anistropic B-factors. > > > > Resolution > > Tony, I have tried to be objective with choosing the resolution. > Recently I have naively published some structures at a lower resolution > than they are. Now, I pretty much only use CC1/2 in the highest resolution > shell to determine the resolution of my dataset, i.e. 0.3<CC1/2<1 ( > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ and > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/), the AIMLESS > output also shows the individual CC1/2 for h, k and l. Lowering the > resolution might give nicer-looking refinement statistics but they are > unrealistic. My frustration is that a culture of doing this means that when > someone does try to publish something at its true resolution the statics > will look worse than previously published structures that claim to be at > the same resolution. > > > > Petri, I think it was the limit of the detector distance so I couldn’t > collect at a higher resolution :( > > > > Thanks again, > > Guto > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > -- > -- > Paul Scherrer Institut > Tim Gruene > - persoenlich - > OSUA/204 > Forschungsstrasse 111 > CH-5232 Villigen PSI > phone: +41 (0)56 310 5297 > > GPG Key ID = A46BEE1A > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
