[phenixbb] HKL2000 behaved weirdly

Diana Tomchick Diana.Tomchick at utsouthwestern.edu
Thu Aug 15 15:49:06 PDT 2013

This happens if the unit cell constants are very small (10 Angstroms or less). It's an indication of a difficulty in finding the proper auto-indexing matrix. It could be caused by many things, without seeing your data it is impossible to tell the actual cause. Potential causes:

1) Not enough spots to accurately determine autoindexing matrix
2) Crystal is actually a small molecule and not a protein (small peptides qualify here)
3) You did not do a peak search on a wide enough oscillation range (at least 1.0 degree and better yet, 1.5 degree-do a peak search on several successive images)
4) Your crystal is not single
5) You also have diffraction from ice or salt crystals and that is creating problems (solution: restrict the resolution to 4.0 Angstroms prior to indexing, then change the resolution to the edge of the detector once you are refining parameters)
6) You accidentally have the crystal aligned perfectly along a zone, and HKL2000 is having difficulties determining the reciprocal lattice constant that is colinear with the X-ray beam (solution: check to see if you can autoindex using frames that were collected 10-30 degrees away from the zone.)
7) Combinations of the above reasons

Try reading the online manual on the HKL research web site to help you determine strategies for how to account for the above difficulties.


Diana R. Tomchick
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214B
Dallas, TX 75390-8816
Diana.Tomchick at UTSouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Mengbin Chen [mengbinc at sas.upenn.edu]
Sent: Thursday, August 15, 2013 2:12 PM
To: PHENIX user mailing list
Subject: [phenixbb] HKL2000 behaved weirdly

Dear All,

I used HKL2000 to index my data, but weird things happened: after I hit peak search, the data were selected to index, and I chose primitive triclinic to continue. After I hit refine, the circles for peak search disappeared, and if I hit "Bravais Lattice", the table would not show up, which meant that I could not proceed to refine in the potentially correct Bravais Lattice. I don't know if anyone else has encountered this problem before, so any suggestions would be greatly appreciated!

Thank you in advance,

Mengbin Chen
Department of Chemistry
University of Pennsylvania


UT Southwestern Medical Center
The future of medicine, today.

More information about the phenixbb mailing list