- Regarding very low or very large unit cell after indexing in HKL2000 : This behavior can be triggered by having either too many reflections (too many increases the chance that some are artefacts which are going to misled the indexing), or too few, respectively.
Editing the peak search results accordingly should help. Sometimes it is useful to use other strategies. For instance scan the images and look for "cleaner" ones (5 images at 0.1° each won't help within a small set). The trick is to index correctly a specific frame *anywhere* in the data set than use the integration parameters from this one frame to integrate the whole pack in one swell run. Another approach : sometimes satellite(s) yield detectable diffraction at low resolution but not at higher resolution. In this case you may choose a higher low resolution limit as the diffraction pattern warrants. "Integrating by 5" may more appropriate in your case. Once comment about helical data collection : in unusual situations (I've seen it occurring only for 1 system so far) the crystal has such mosaicity that the changes of orientation between two different pieces of crystals are elevated. HKL2000 may lose the indexing in the middle of the run. This requires that you process the datasets in several parts. Nonetheless you should not have to go back to indexing every 5 frames. Be sure to properly parameter scaling to the 5 frame per pack data collection approach. Hope this is of use. Good luck Thierry -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Christopher Barnes Sent: Thursday, April 16, 2015 4:38 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] XDS Processing with Translated Detector and Radiation Sensitive Crystals Hi all, I am having trouble processing synchrotron data with XDS for a large unit cell protein complex (Spacegroup P2, Cell 225 x 256 x 430). My crystals diffract to 3.1 Angstrom, but at this resolution we had significant spatial overlaps. To alleviate this we translated the detector 40 mm in both the x and y directions to achieve higher resolution at a distance of 850mm (on a Pilatus 6M detector), as well as used fine slicing (0.1 degree) for data collection. In addition, our crystals are highly radiation sensitive, so we use vector data collection strategies to expose untouched crystal volumes to the beam to maintain high resolution diffraction. This usually allows us to get 5 frames/spot before moving to a new location due to radiation damage. However, during my processing with XDS, integration results in very low I/sigma, even at low resolution (ie a value of 1.8), even though we have high intensity reflections that are significantly above the background. Looking at the INTEGRATE.LP and CORRECT.LP, with the refined unit cell parameters the standard deviation of spot pixels is 1.15 and standard deviation of spindle position is 0.20. However, the average three-dimensional profile of strong reflections is usually missing "spots" in 3-4 out of the 9 boxes. A check of the detector origin corresponds with the new beam position (967, 1511) in all the log files. Any help or insight into processing with a translated detector or radiation sensitive crystals would be helpful. We have tried to use HKL and iMosflm, but neither program provides a consistent indexing solution (usually can identify a & b dimensions correctly, but they widely vary in c dimension, sometimes very low (ie 35) or sometimes very high (ie 660). Thanks, Christopher Graduate Student - Department of Structural Biology University of Pittsburgh - School of Medicine 3501 Fifth Avenue BST3, Rm 1043 Pittsburgh, PA 15260 email: co...@pitt.edu work: 412-648-8542 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
