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

[Tom Goddard]

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.

	Tom


> 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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