If you had that crystal saved after earlier collection then recollect a dataset again to see if the same Y-Chi2 profile is observed.
On Mon, Jun 27, 2011 at 4:59 PM, bie gao <[email protected]> wrote: > Jim, that's the first thing I tried - triclinic gave similar Y-Chi2 > profile. > Shiva, not sure what you mean by collecting the same crystal again (thaw > and remount?). But I collected 180 degrees, Chi2 seems to correlate with > rotation angle. > > Cheers, > > > On Fri, Jun 24, 2011 at 1:39 PM, Jim Pflugrath > <[email protected]>wrote: > >> ** >> 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:[email protected]] *On Behalf Of >> *Shiva Bhowmik >> *Sent:* Friday, June 24, 2011 11:42 AM >> >> *To:* [email protected] >> *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 <[email protected]> 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 < >>> [email protected]> 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 <[email protected]> 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 >>>>> >>>> >>>> >>> >> >
