Hi all, There is a good news and it is that we have got crystals this morning which have diffracted upto 2.5 ang at home source and data collection is going on. I hope this solves the problem though the not so good anomalous signal at home source will probably make SAD phasing difficult. However to provide some additional information asked for by Prof. Francis E Reyes:
The data is in all probability twinned because of two reasons: 1) At the time of data collection the two fused crytsals( or crystallites?) could be seen clearly which unfortunately could not be separated. 2) The data shows clear interference of lattices with one lattice showing much higher intensity for the first half or so of the 360 images collected and the other lattice for the second half. I have tried separating the frames and solving but it didnt work out. The spacegroup is P41212 in all data. The synchroton data has resolution of 2.75 ang collected at 1.60428 ang wavelength and the home data 3.0 ang. collected at CuKalpha wavelength. All are Co soaks. I should restate that it is a DNA oligomer and though I have been able to get heavy atom positions and the occupancies look ok but the phased map is too noisy to be interpreted. Regards, ARKO On Fri, Jan 20, 2012 at 9:46 PM, Francis E Reyes <francis.re...@colorado.edu > wrote: > Let's have some more info here. > > What resolution we talking about? What are the space groups? > > What is the nature of the Co (is it a heavy atom soak?, a bound Co?) > > Have you tried to find heavy atom sites? (anomalous Patterson, or some > other automated method) > > Are they believable? > > You say the data set is twinned. How do you know this is the case? > > You're looking for help (and you've come to the right place) but knowing > a little bit more about your system will help others suggest a suitable > phasing scenario. > > F > > > > > > On Jan 19, 2012, at 12:39 PM, arka chakraborty wrote: > > > Hi all, > > > > Thanks a lot for the valuable suggestions.I have tried detwinning it > but the detwinning program in CCP4 takes care of only merohedral data( if > I am not wrong) and the other program( I guess Cell-now in Apex 2 by > Bruker?) which takes care of non-merohedral twinning is not accessible to > it( as I can't buy it). Also, the anomalous signal in the home source data > is pretty weak. So, I was thinking about trying to get a better result by > trying to merge the two data sets, though I am aware of the problem posed > by twinning. But since we were not being able to get crystals of size > mountable at home source, I thought why not try whatever is possible! > > > > Thanking you, > > > > Regards, > > > > ARKO > > > > On Thu, Jan 19, 2012 at 10:13 PM, James Holton <jmhol...@lbl.gov> wrote: > > > > Oh dear. > > > > You definitely cannot de-twin a dataset by mergeing it with a > non-twinned dataset! And if the twin fraction of your synchrotron set is > much greater than 0.3 then it is unlikely that you will be able to use the > anomalous differences to solve the phase problem. > > > > If I were you, I would focus on the non-twinned crystal system. You CAN > average anomalous differences across different crystals, provided they are > reasonably isomorphous. http://dx.doi.org/10.1107/S0907444910046573 > > > > And I should add the caveat that twinning is equivalent to > "non-isomorphism" until after you have solved the structure because it > dramatically changes the intensity you have available for any given hkl > index. > > > > -James Holton > > MAD Scientist > > > > > > On 1/19/2012 8:20 AM, arka chakraborty wrote: > >> Hi all, > >> > >> Thanks for providing multiple solutions to my problem. Prof . Tim > Gruene and Prof. James Holton provided some nice solutions. However since > the data are collected from different crystals, I am not sure whether I can > do MAD phasing. My aim is to merge the two data-sets to circumvent the > problem posed by the fact that the synchroton data is twinned. So maybe > merging the data sets will provide better phases from SAD phasing? My > main concern was how to do scaling adjustments before using the data-sets > together. > >> > >> Thanking you, > >> > >> Regards, > >> > >> ARKO > >> > >> On Thu, Jan 19, 2012 at 1:46 AM, Soisson, Stephen M < > stephen_sois...@merck.com> wrote: > >> But if we were to follow that convention we would have been stuck with > Multi-wavelength Resonant Diffraction Experimental Results, or, quite > simply, MuRDER. > >> > >> > >> > >> -----Original Message----- > >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Jacob Keller > >> Sent: Wednesday, January 18, 2012 3:13 PM > >> To: CCP4BB@JISCMAIL.AC.UK > >> Subject: Re: [ccp4bb] Merging data collected at two different wavelength > >> > >> This begs the question* whether you want the lemmings to understand > >> you. One theory of language, gotten more or less from Strunk and > >> White's Elements of Style, is that the most important feature of > >> language is its transparency to the underlying thoughts. Bad language > >> breaks the transparency, reminds you that you are reading and not > >> simply thinking the thoughts of the author, who should also usually be > >> invisible. Bad writing calls attention to itself and to the author, > >> whereas good writing guides the thoughts of the reader unnoticeably. > >> For Strunk and White, it seems that all rules of writing follow this > >> principle, and it seems to be the right way to think about language. > >> So, conventions, even when somewhat inaccurate, are important in that > >> they are often more transparent, and the reader does not get stuck on > >> them. > >> > >> Anyway, a case in point of lemmings is that once Wayne Hendrickson > >> himself suggested that the term anomalous be decommissioned in favor > >> of "resonant." I don't hear any non-lemmings jumping on that > >> bandwagon... > >> > >> JPK > >> > >> *Is this the right use of "beg the question?" > >> > >> > >> > >> > >> > >> On Wed, Jan 18, 2012 at 1:57 PM, Phoebe Rice <pr...@uchicago.edu> > wrote: > >> >> > >> >>> Can I be dogmatic about this ? > >> >> > >> >>I wish you could, but I don't think so, because even though those > >> >>sources call it that, others don't. I agree with your thinking, but > >> >>usage is usage. > >> > > >> > And 10,000 lemmings can't be wrong? > >> > >> > >> > >> -- > >> ******************************************* > >> Jacob Pearson Keller > >> Northwestern University > >> Medical Scientist Training Program > >> email: j-kell...@northwestern.edu > >> ******************************************* > >> Notice: This e-mail message, together with any attachments, contains > >> information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > >> New Jersey, USA 08889), 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. > >> > >> > >> > >> -- > >> > >> ARKA CHAKRABORTY > >> CAS in Crystallography and Biophysics > >> University of Madras > >> Chennai,India > >> > > > > > > > > > > -- > > > > ARKA CHAKRABORTY > > CAS in Crystallography and Biophysics > > University of Madras > > Chennai,India > > > > --------------------------------------------- > Francis E. Reyes M.Sc. > 215 UCB > University of Colorado at Boulder > > > > > > -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*
