Instead of an imperfect crystal, this can also occur if one chooses the wrong Bravais lattice type (or spacegroup) to integrate. For example, if you choose tetragonal when it is really orthorhombic with a ~ b, or if you choose orthorhombic and beta is 90.2, then you can see that trying to force that unit cell will lead to higher residuals during positional refinement. If one reciprocal lattice is oriented mostly along Y, then I think what Bing observes can happen in such cases. This is easily tested by integrating in triclinic.
_____ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Shiva Bhowmik Sent: Friday, June 24, 2011 11:42 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Y-Chi2 running out of chart Hi Bie, Curious to know what are the cell parameters obtained after scaling? You mention observing perfect Chi2 statistics with lysozyme crystals. But are you observing the same Chi2 statisctis with the crystal that yielded unusual Y-Chi2 if you collect another dataset. If there is a consistency of observing the unusual Y-Chi2 with that crystal again then it is likey that the crystal maybe highly imperfect. If not, then there could have been a one time un-nailed problem occurred during that collection. Cheers, Shiva On Thu, Jun 23, 2011 at 8:59 AM, bie gao <gao...@gmail.com> wrote: Dear colleagues, thank you all for your help! I really appreciate it. I did perform a lysozyme test after the repair. I collected ~50 degree (99%). Everything seems to be fine. Maybe I should have done it for an entire round. As for the current collection, as I suspended, it did go out of the chart but then came down to normal. Overall Rmerge is 7.9% (4% square). As Zbyszek and others mention, it is probably due to imperfect crystal and also uneven cooling. If our field engineer discovers anything else, I'll post it here. Thanks again for your help. On Wed, Jun 22, 2011 at 9:00 PM, Artem Evdokimov <artem.evdoki...@gmail.com> wrote: As a follow up to the excellent suggestions made by others I would suggest that a close examination of x-file headers may reveal abnormalities in e.g. crystal orientation -- suspecting an unlocked or drifting goniostat. It may also indicate a precession around the phi, which should also manifest itself in a systematic deviation of average intensities (i.e. scale factors) in a similar pattern (assuming uneven illumination of the crystal). Sometimes the precession is caused by a bubble or a tiny chunk of ice trapped under the pin, it can melt unevenly and re-align the pin a few minutes into the run (something similar used to happen a lot at one or two beam lines and it drove me nuts until I figured out the need to re-align the crystal after the initial screening). Artem On Wed, Jun 22, 2011 at 11:22 AM, bie gao <gao...@gmail.com> wrote: Dear Colleagues, I'm collecting a dataset on our recently repaired Rigaku home source. Crystal diffracts to 2.2A. Indexing seems to be all fine. However, during integration, I realize Y-Chi2 is increasing constantly (from 2 to 4.5, almost linear) within 60 degree collection, whereas X-Chi2 stays the same. An image is attached. There are still another 60 degree to go. Although the prediction fits the images well so far, I'm afraid the Y-Chi2 will eventually run out of the chart. My question is could it be related to any hardware malfunctioning, i.e., goniometer, image plates, etc, which may be a side effect of the recent major repair? Or what else it can be? Thanks, Bing
