Sorry for being late in replying, but thank you all for your suggestions! The resolution is ~3 angstroms, so it was quite easy to pick more than 100 peaks for indexing. So I tried to index ~5-6 images at the same time as you suggested, the Bravais Lattice window appeared (and I reset the beam center too), but the unit cell dimensions were ~10 angstroms along one axis, which was not appropriate since the protein is around 40 kDa. I tried to manually pick peaks for indexing, still cell dimensions were too small to be properly assigned. I feel the crystal has got severe problems of multiple lattices and high mosaicity at the same time, which made it hard to index. I am still playing around with the dataset to see if I can get any luck with it, so I'll let you know if I can work this out.

Mengbin

On Fri, Aug 16, 2013 at 12:18 PM, Noinaj, Nicholas (NIH/NIDDK) [F] <noinajn@niddk.nih.gov> wrote:

Mengbin,

This happens in HKL2000 with tough datasets. The data can sometime appear to be very nice, possibly some high mosaicity, but still not process properly. I have seen this many times. As mentioned already, the next step is to start trying different things to get the data to process. WIthout knowing more about resolution, etc, here is a few things to try.

1- Check and the double check the beam center. Then, check it again! With troublesome datasets, this is EXTREMELY important. In HKL2000, everytime you hit Abort Refinement, you have to reset the beamcenter again. SO monitor the beam center and everytime it gets too far away from the actual numbers, reset it.

2- you want to try to have roughly 100 peaks for indexing at minimum (if possible), so change the resolution limits to 15 ang - 4 ang, then retry indexing. IF this does not work, try 15-5ang, then 12-5, then 10-5, etc.

3- If #2 doesn't work, then you can alway try indexing using multiple frames, esp if you don't have a enough peaks on the first frame. To do this, please see the HKL2000 manual, or let me know, i can send you some screenshots or give you a call to guide you via phone. here, you can use 5-10 frames for indexing if needed.

4- as a last option, you can always manually select your peaks. i have had this work nicely in the past, but again, last option.

5- you could try other data processing programs too such as MoSFLM, XDS, Xia2, etc.

If you still don't get it working, i am more than happy to take a quick look. Just send me one of your frames to analyse. Of course, everything will be strictly confidential. Thanks in advance and good luck!

Cheers,
Nick

________________________________
From: Mengbin Chen [mengbinc@sas.upenn.edu]

Sent: Thursday, August 15, 2013 3:12 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

--
Mengbin Chen
Department of Chemistry
University of Pennsylvania

--
Mengbin Chen

Department of Chemistry

University of Pennsylvania