[Chimera-users] How to prepare increase visible detail characteristics in cryo-EM structure with chimera?

Tom Goddard goddard at sonic.net
Tue Aug 4 10:07:19 PDT 2020

Hi Yeping,

  That figure from Nature uses ChimeraX, not Chimera.  ChimeraX is the successor to Chimera.  ChimeraX has better lighting.  In ChimeraX uses soft lighting,  Also make sure step size is 1 in the Volume Viewer panel to show data at full resolution.  And use a high enough threshold level so helices have space between them.


> On Aug 4, 2020, at 9:45 AM, sunyeping <sunyeping at aliyun.com> wrote:
> Dear all,
> I am trying to learn preparing publishable figures of cryo-EM protein structure. I try to reproduce a figure (fig. 4A) from a paper published in Nature (https://doi.org/10.1038/s41586-020-2571-7).
> Could you please find the original figure in the publication and the one I prepared in the following link?
> https://drive.google.com/file/d/1dwQYT9-bGbs7OHi8e351SmE0FYr6FLK4/view?usp=sharing
> The original figure (a) is for EMD-22156. I download the map for EMD-22156 form https://www.ebi.ac.uk/pdbe/emdb/ <https://www.ebi.ac.uk/pdbe/emdb/>, loaded it in Chimera, adjusted the range, hide the dusted, performed segmentation, and get images like (b). 
> The orignal figure (a) has plenty of structural detailed, and the helix can be clearly seen, but the images I prepared do not like that and look ugly. 
> Could you give me some detailed step-by-step instruction on how this original figure was prepared in chimera?
> With many many thanks
> Yeping Sun  
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