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