Real space refine of long side chains
I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards... Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom [email protected] tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab
Hi Luca,
I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards...
do you have an example that you can share (off list)? Ideally, the most helpful would be to have models before and after refinement, the map and chain/residue ids of problematic side chains. Pavel
Hi Luca,
I had similar issue with refinement against a low resolution data. However,
choosing input model as reference model for restraints (with little bit of
playing around with weight factor) took care of this.
Ashu
On Mon, Nov 25, 2019 at 2:12 PM Luca Pellegrini
I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards...
Best wishes, Luca
Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom
[email protected] tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab
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participants (3)
-
Ashu Sharma -
Luca Pellegrini -
Pavel Afonine