How to prepare increase visible detail characteristics in cryo-EM structure with chimera?
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=s... The original figure (a) is for EMD-22156. I download the map for EMD-22156 form 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
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@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=s...
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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Yeping, There is a ChimeraX example image and short command script with soft lighting on a cryoEM map here: <http://www.rbvi.ucsf.edu/chimerax/features.html#ambient-em> The Nature figure also has white background and silhouettes (black outlines). In ChimeraX you can just click icons in the toolbar across the top of the window to get these settings. In the Graphics tab of the toolbar, click the white square icon for white background, and the seahorse icon to turn outlines on and off. ChimeraX toolbar Graphics tab: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/graphics.html> Making images in ChimeraX: <http://rbvi.ucsf.edu/chimerax/docs/user/images.html> We also have a chimerax-users@cgl.ucsf.edu mailing list, so if you have questions about ChimeraX later that will be a better address. I hope this helps, Elaine
On Aug 4, 2020, at 10:07 AM, Tom Goddard <goddard@sonic.net> wrote:
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@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=s...
The original figure (a) is for EMD-22156. I download the map for EMD-22156 form 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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
sunyeping -
Tom Goddard