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 <jim.pflugr...@rigaku.com>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: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 >>>> >>> >>> >> >
