DNA basepairing restraint refinement
Hi, I am working my low resolution data (6A) by MR and met a problem about DNA basepairing during refinement. I think so far everything looks OK except the bases flipped during the refinement. I added basepairing restraint for all bases, however, seems not help too much. Does anyone have experience on that? Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：[email protected]
On Fri, Apr 18, 2014 at 6:53 AM, 李翔
I am working my low resolution data (6A) by MR and met a problem about DNA basepairing during refinement. I think so far everything looks OK except the bases flipped during the refinement. I added basepairing restraint for all bases, however, seems not help too much. Does anyone have experience on that?
First of all, make sure you have real-space refinement turned off; this may be moving the DNA too aggressively. Second, it sounds like the base-pairing restraints may not be working correctly. If you send me the model (off-list!) I can take a look and see if there is a bug. The other option is to restrain the coordinates to the starting structure - I think the reference model restraints would be best but I'm not entirely sure if they work for DNA. (If not, you can use harmonic restraints, but these are less flexible.) -Nat
Hi Xiang, can you please send me data and model files so I can have a closer look? If as you say you used base-pair restraints they should not flip, and if they do this tells me there is something wrong with base-pair restraints, and so to investigate this I'd like to see the files. Thanks, Pavel On 4/18/14, 6:53 AM, 李翔 wrote:
Hi,
I am working my low resolution data (6A) by MR and met a problem about DNA basepairing during refinement. I think so far everything looks OK except the bases flipped during the refinement. I added basepairing restraint for all bases, however, seems not help too much. Does anyone have experience on that?
Sincerely, Xiang
participants (3)
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Nathaniel Echols -
Pavel Afonine -
李翔