<div dir="ltr">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.<div>
<br></div><div>Mengbin<br><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Aug 16, 2013 at 12:18 PM, Noinaj, Nicholas (NIH/NIDDK) [F] <span dir="ltr"><<a href="mailto:noinajn@niddk.nih.gov" target="_blank">noinajn@niddk.nih.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Mengbin,<br>
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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.<br>
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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.<br>
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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.<br>
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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.<br>
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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.<br>
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5- you could try other data processing programs too such as MoSFLM, XDS, Xia2, etc.<br>
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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!<br>
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Cheers,<br>
Nick<br>
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________________________________<br>
From: Mengbin Chen [<a href="mailto:mengbinc@sas.upenn.edu" target="_blank">mengbinc@sas.upenn.edu</a>]<br>
<div>Sent: Thursday, August 15, 2013 3:12 PM<br>
To: PHENIX user mailing list<br>
Subject: [phenixbb] HKL2000 behaved weirdly<br>
<br>
</div><div><div>Dear All,<br>
<br>
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!<br>
<br>
Thank you in advance,<br>
Mengbin<br>
<br>
--<br>
Mengbin Chen<br>
Department of Chemistry<br>
University of Pennsylvania<br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Mengbin Chen<div>Department of Chemistry</div><div>University of Pennsylvania</div>
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