Hi all,
Actually, what I think has happened here is that Phaser has limited the resolution to what it estimated was needed to get a clear enough solution, and then the final refinement was carried out with all the data. The signal-to-noise is lower with limited data, but it’s a price that seems worth paying to get the answer more quickly. The final refined LLG of 1848 is a very large number, and the TFZ-equivalent calculation indicates that, if the translation search had been carried out with the final refined orientation using all the data, the TFZ would have been a very respectable 30.2. That’s probably a better number to look at now, with the new adaptive Phaser searches.
Of course, I agree completely that you would also like to see that the correct space group gave a much higher score with the same data than the alternative space groups! Phaser chose a single solution, so it was probably at least reasonably clear.
We’re stlll working on how to give the clearest possible indication at the end of a run as to whether you should be confident that it is correct.
Best wishes,
Randy Read
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
On 28 Jan 2015, at 19:33, Matthew Franklin <[log in to unmask]> wrote:
> Hi Jeorge -
>
> Something seems to have changed for the worse in this MR run. In your earlier posting, where you failed to find a solution in P222, your log file had solutions with RFZ=23.4, generally a clear indication of a correct rotation function solution. (You didn't include this log file as text, so I can't extract the relevant lines to show you.) But in this run, your log file shows a solution with RFZ=5.7, which is much more marginal. The space group choice for the translation function shouldn't affect the results of the rotation function. What else did you vary - is the search model different?
>
> In addition to what Roger suggested, other indications that you have the right solution come from the translation function tables. You should have a very clear distinction between the correct solution and incorrect solutions, like this:
>
>> Fast Translation Function Table: Space Group C 1 2 1
>> ----------------------------------------------------
>> #SET #TRIAL Top (Z) Second (Z) Third (Z) Ensemble
>> 1 1 4328.56 (29.62) - - - - 3gi8_fab
>> 1 2 4294.35 (26.16) - - - - 3gi8_fab
>> 1 3 4252.29 (27.13) - - - - 3gi8_fab
>> 1 4 3746.99 (13.34) 3725.62 (12.73) - - 3gi8_fab
>> 1 5 3467.72 ( 5.02) 3467.43 ( 5.02) 3464.58 ( 4.94) 3gi8_fab
>> 1 6 3545.59 ( 6.93) 3482.22 ( 5.27) - - 3gi8_fab
>
> Trials 1-3 are correct, while trials 5-6 are incorrect. (Trial 4 is probably also correct, but wasn't tested further by Phaser.)
>
> You also want to check that the packing test did not throw out one of these high-scoring translation solutions (e.g. your RFZ=23.4 solution). If that happened, this could mean you need to trim away some loops in your search model.
>
> Good luck,
>
> Matt
>
>
>
> On 1/28/15 12:25 PM, jeorgemarley thomas wrote:
>> Hi, all
>>
>> As per the suggestions, I hv done with the phaser MR and the solution has come with screw axes P 21 21 21. here I am attaching the output text from Mr and sol file. So Now should I go ahead with this? Please suggest.
>>
>> Thank you very much in advance !
>>
>> On Tue, Jan 27, 2015 at 9:33 PM, jeorgemarley thomas <[log in to unmask]> wrote:
>> Thank you so much to all for your kind concern.
>>
>>
>>
>> Jeorge
>>
>> On Mon, Jan 26, 2015 at 5:55 PM, Kay Diederichs <[log in to unmask]> wrote:
>> Dear Jeorge,
>>
>> you'll find some information about this in http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination . A practical and easy way is described in http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless
>>
>> HTH,
>>
>> Kay
>>
>> On Mon, 26 Jan 2015 11:24:27 +0100, Tim Gruene <[log in to unmask]> wrote:
>>
>> >Dear Jeorge,
>> >
>> >XDS make no claim to determine the SPACE GROUP but rather the LAUE
>> >GROUP, as only the latter is taken into account during data integration.
>> >
>> >This is definitely so during the indexing step (IDXREF.LP), but even in
>> >CORRECT, when systematic absences are sometimes indicated, XDS does not
>> >really choose the space group.
>> >
>> >Best,
>> >Tim
>> >
>> >On 01/26/2015 05:46 AM, jeorgemarley thomas wrote:
>> >> Hello Dr. Randy
>> >> Here is the IDXREF.LP I got in which, on the basis of quality of fit, I
>> >> went for this space group well I would also try for the other screw axes.
>> >> So should I Integrate the data from beginning with all possible screw axes
>> >> of orthogonal space group? I am attaching the IDXREF.LP screen shot here.
>> >>
>> >> Jeorge
>> >>
>> >> On Sun, Jan 25, 2015 at 5:00 PM, Roger Rowlett <[log in to unmask]> wrote:
>> >>
>> >>> Did you search all 8 possibilities of screw axes, e.g. P2221, P21212,
>> >>> P212121, etc?
>> >>>
>> >>> Roger Rowlett
>> >>> On Jan 25, 2015 4:50 AM, "jeorgemarley thomas" <[log in to unmask]>
>> >>> wrote:
>> >>>
>> >>>> Hi, I have processed the data using XDS and space group found to be P 2 2
>> >>>> 2 (16) and I used the phaser MR for first phase determination. The model I
>> >>>> have used has has more than 70 % sequence identity, when I run the phaser I
>> >>>> got the message which I have attached here. And only sum. file I got as an
>> >>>> output. Does any one have suggestion what should I do ? I would highly
>> >>>> appreciate your kind suggestions. Thank you in advance.
>> >>>>
>> >>>>
>> >>>>
>> >>
>> >
>> >--
>> >Dr Tim Gruene
>> >Institut fuer anorganische Chemie
>> >Tammannstr. 4
>> >D-37077 Goettingen
>> >
>> >GPG Key ID = A46BEE1A
>> >
>> >
>>
>>
>
>
> --
> Matthew Franklin, Ph. D.
> Senior Scientist
> New York Structural Biology Center
> 89 Convent Avenue, New York, NY 10027
> (212) 939-0660 ext. 9374
>
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