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
<kirtswab...@gmail.com <mailto:kirtswab...@gmail.com>> wrote:
Thank you so much to all for your kind concern.
Jeorge
On Mon, Jan 26, 2015 at 5:55 PM, Kay Diederichs
<kay.diederi...@uni-konstanz.de
<mailto:kay.diederi...@uni-konstanz.de>> 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
<t...@shelx.uni-ac.gwdg.de <mailto:t...@shelx.uni-ac.gwdg.de>> 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
<rrowl...@colgate.edu <mailto:rrowl...@colgate.edu>> 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"
<kirtswab...@gmail.com <mailto:kirtswab...@gmail.com>>
>>> 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
