[3dem] Resolution estimate: FSC vs PDB modeling

[Qiu-Xing Jiang]

Hi Hongwei,
We tried that. There was something strange in the HRnoised dataset I generated because it changed the converging the symmetry parameter slightly after the refinement. I am checking into it, whether the compilation of the program did something. The other program being used is the ResMap recently developed by the Yale trio.
Thanks.
Qiu-Xing


From: Hongwei Wang <hongweiwang at tsinghua.edu.cn<mailto:hongweiwang at tsinghua.edu.cn>>
Date: Wednesday, March 12, 2014 9:07 AM
To: qx jiang <qiu-xing.jiang at utsouthwestern.edu<mailto:qiu-xing.jiang at utsouthwestern.edu>>, "3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>" <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>>
Subject: Resolution estimate: FSC vs PDB modeling

Hi, Qiu-Xing,

You may want to try the method that Richard Henderson and his colleagues described most recently in their Ultramicrosopy paper: http://www.ncbi.nlm.nih.gov/pubmed/23872039

Best,
Hongwei


Dear colleagues,
This has been a topic discussed in a couple of map validation papers. I have a scenario encountered in a recent project and would like some input from those interested.
We had a filament complex reconstruction, made of a small protein whose crystal structure contains mainly loops held together in the core by three pairs of disulfide bonds. At the time of resolution estimation, we used two independent maps calculated from either randomly selected halves or top/bottom halves to calculate FSC as usual in SPIDER. The FSC0.5 of the former gives 9.2 angstroms, which is more conservative than the FSC0.143 of the latter, and was used as a nominal estimate.

The other opinion  from a senior colleague was PDB modeling, whose operations are to dock the X-ray structures of individual units into the map (assuming no change), filter the resulted PDB model to different resolutions, and visually determine at which resolution the map calculated from the PDB model and the experimental density map match the best(at certain thresholds), and could then be used for resolution estimate. When we were operating this procedure, we knew that our filaments had lipids associated and our map was not good enough to resolve the loops on the surface of the individual units in the filament. To make  the two maps match well to our eyes, we had to filter both to 12-15 angstroms, which would then say the resolution was 12-15 A. The calculated cross-correlation between the map from the pdb model and the experimental map was high at 9.2-15 range, but we were not sure whether it would be decisively meaningful.

We had debates and disagreements on which to report. At the end we decided to use FSC0.5 as usual, and refrained from interpreting the map with mutations at the subunit interface due to the experience of PDB modeling. I  wonder if some of you had similar experience, and more generally whether PDB modeling is suitable to replace FSC.

Thanks for sharing your experience.

Best regards,

Qiu-Xing



________________________________

UT Southwestern Medical Center
The future of medicine, today.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mail.ncmir.ucsd.edu/mailman/private/3dem/attachments/20140312/3dbd5cce/attachment.html>