Dear all, after a week looking more closely into the datasets, also with the help of Manfred Weiss and Kay Diederichs, who kindly offered to look at some of them, I come back to you to report on our findings (should this info be useful in the future to any of you). Thank you very much everybody for your replies. :)
I have 11 datasets, collected from 3 very small crystals (30-40 um aprox). While the highest resolution for the "best datasets" extended to 4 or 4.5 Angstroms, two aspects that contributed to the difficulty in processing were: radiation damage and also the presence of multiple lattices. It was necessary to look through the images and select the wedges where there were (single) spots at "high resolution" (often after only 180 degrees of data collection the crystals were considerably damaged and attempts to process the 360 degrees that were collected didn't work or resulted in extremely poor overall statistics). For the indexing of multiple lattices I have had the opportunity to try programs like CrysalisPro from Rigaku and Proteum from Bruker (sorry I didn't try DIALS yet, although I was advised to do it too!) and I can tell that they do a fine job in finding the crystal lattice despite the ugliness of the spots. However, since only small wedges of the data were useful and I have a low symmetry space group, I couldn't take great advantage of their capabilities, though. In some of the datasets, we could also see that indexing of few frames gave ok statistics, but as more and more frames were added to the processing (also as the presence of the second lattice became more evident) the statistics became worse. With the exception of 3 datasets (belonging to the same crystal), were the spots were streaky/multiple/splitted, the others could be treated to a greater or a lesser extent and processed with the XDS.INP file resulting from generate_XDS.INP. Also, the fact that many spots were selected by COLSPOT but very few were used in the IDXREF step was due to the fact that I had some ice rings (how could I miss that, right?) and many were picked from there. So, once again, carefully selecting the SPOT_RANGE or defining it more than once, as well as using the keyword EXCLUDE_RESOLUTION_RANGE where the ice rings were, or simply cutting the resolution at 4 Angstroms, alleviated the problem in most cases. Kay also advised me to use DELPHI=20, which is used during the INTEGRATE step, and although its default is 5, it's good to increase its value in instances where there are few strong reflections that can be used for learning spot profiles (avoids geometry refinement with too few reflections in INTEGRATE). With the data that I have, very weak, I was also advised by Kay not to lower the MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT below 3 - but rather to increase it to 6 if my reflections were big. And if the latter was done (MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=6) lower STRONG_PIXEL to 3. Although the first instinct from many of you was to think that there was something wrong with the input, like detector distance, origin, oscillation range, etc., all these parameters were recorded correctly. I think that the fair way to summarize this all is "it's crappy data" (for a number of reasons), because the programs and the synchrotron software did their job fine. So thank you once again everyone for helping me and participating in this discussion, I will now go back to the lab and try to grow nicer, better ordered, bigger crystals ;) All the best, Almu El vie., 29 nov. 2019 a las 14:43, Tim Gruene (<tim.gru...@univie.ac.at>) escribió: > Dear Almudena, > > SPOT_MAXIMUM-CENTROID is probably the keyword in XDS.INP that you want to > increase in your situation. The default is 3. Try e.g. 5, and increase > slowly > to make sure that the suggested solution makes sense > > Best regards, > Tim > > On Friday, November 29, 2019 12:48:11 PM CET Almudena Ponce Salvatierra > wrote: > > Dear all, > > > > I have some data sets that don't want to be processed :p > > > > In one of them, when I look at IDXREF.LP I see virtually none of the > found > > spots were indexed and the reason is that they are "too far from the > > expected position". The spots are smeary and elongated, so not the > > prettiest. > > > > I have managed to process so far only one data set with decent statistics > > from another crystal harvested from the same drop, where the diffraction > > spots look better. > > > > I am trying to find in the xds wiki the keyword I should fine tune in > order > > to make those spots indexable. > > > > Could you help me please? > > > > Thank you very much in advance. > > > > Best wishes, > > > > Almu > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > 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
