On Mon, May 7, 2012 at 8:46 AM, Kelly Daughtry wrote:

Looking at the P422 data, it look like you have pseudo translational symmetry. Did you try processing this data as I422?

From the P422_xtriage.log:

The full list of Patterson peaks is:

  x      y      z            height   p-value(height) ( 0.500, 0.500, 0.165 ) :   78.635   (6.634e-07) ( 0.000, 0.000, 0.330 ) :   56.292   (2.795e-05) ( 0.500, 0.500, 0.497 ) :   30.920   (1.207e-03)

One word of caution: an exceptionally high off-origin peak can mean that the unit cell was measured too large, and you've integrated extra reflections that are really non-existent. (I'm not sure what the threshold for this is, but 80% seems pretty large.) Splitting and various indexing artifacts can sometimes lead to this. I'd recommend running labelit.index on the images and seeing what it thinks the lattice should be. -Nat

Hi Kelly and Nat, Thanks for your quick reply. The two space groups come out depending on which frames I started to index. Actually, in the P422 xtriage outpout, it stated it could be I422 with C'=C/3: ____________________________________________ The full list of Patterson peaks is: x y z height p-value(height) ( 0.500, 0.500, 0.165 ) : 78.635 (6.634e-07) ( 0.000, 0.000, 0.330 ) : 56.292 (2.795e-05) ( 0.500, 0.500, 0.497 ) : 30.920 (1.207e-03) ( 0.500, 0.500, 0.187 ) : 4.873 (9.347e-01) If the observed pseudo translationals are crystallographic the following spacegroups and unit cells are possible: space group operator unit cell of reference setting I 4 2 2 (a,b,3*c) x+1/2, y+1/2, z+1/6 (191.70, 191.70, 103.68, 90.00, 90.00, 90.00) ____________________________________________________________________ When I indexed as I422, some of the spots were not picked, but scaled data went to 2.65 A; P422 could cover all the spots, but resolution could only reach ~2.9A, however, I did see 5 sigma spots around 2.6/2.7. This might indicate I have a "perfectly" split crystal so that those spots looked like they belong to a P4 space group were actually from other crystals. Regards, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ****************************************************************** -----Original Message----- From: Kelly Daughtry [mailto:[email protected]] Sent: Monday, May 07, 2012 12:50 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Difficult dataset and refinement--P422? I422?Twinning? I agree. The fact that two "crystals forms" appear, with related unit cells: P422 data: unit_cell = 191.6999969 191.6999969 311.0539856 90 90 90 space_group = "P 4 2 2" I422 data: unit_cell = 191.783 191.783 103.775 90 90 90 space_group = "I 4 2 2" indicated to me you have mis-indexed the P422 data. It is likely I422. Kelly ******************************************************* Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 ******************************************************* On Mon, May 7, 2012 at 12:18 PM, Nathaniel Echols wrote:

On Mon, May 7, 2012 at 8:46 AM, Kelly Daughtry wrote:

...

Looking at the P422 data, it look like you have pseudo translational symmetry. Did you try processing this data as I422?

From the P422_xtriage.log:

The full list of Patterson peaks is:

  x      y      z            height   p-value(height) ( 0.500, 0.500, 0.165 ) :   78.635   (6.634e-07) ( 0.000, 0.000, 0.330 ) :   56.292   (2.795e-05) ( 0.500, 0.500, 0.497 ) :   30.920   (1.207e-03)

One word of caution: an exceptionally high off-origin peak can mean that the unit cell was measured too large, and you've integrated extra reflections that are really non-existent.  (I'm not sure what the threshold for this is, but 80% seems pretty large.)  Splitting and various indexing artifacts can sometimes lead to this.  I'd recommend running labelit.index on the images and seeing what it thinks the lattice should be.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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