[3dem] 回复：Re: Exporting a montage map from SerialEM to a single MRC File

["蔡舒君"]

Thank you, Huy and Garry. Both methods work! Sorry for the late feedback.
Best,Shujun

----- 原始邮件 -----
发件人：Huy Bui via 3dem <3dem at ncmir.ucsd.edu>
收件人：Garry P Morgan <Garry.Morgan at colorado.edu>
抄送人："cai_sj at sina.com" <cai_sj at sina.com>, 蔡舒君 via 3dem <3dem at ncmir.ucsd.edu>
主题：Re: [3dem] Exporting a montage map from SerialEM to a single MRC File
日期：2026年02月07日 04点29分

Hi Shujun,

You can stitch the images using imod programs.

Extract coordinate:extractpieces -mdoc MMM.mrc -output MMM.pl
Generate the blended stack (change to bin 1 if you don't want to bin it)blendmont -imin MMM.mrc -plin MMM.pl -imout MMM_bin4_montage.mrc -rootname MMM_bin4 -sloppy -shift -bin 4
Best,
H


On Fri, Feb 6, 2026 at 11:05 AM Garry P Morgan via 3dem <3dem at ncmir.ucsd.edu> wrote:





Shujun,
One way to do this is in SerialEM:  while the map file is loaded on your monitor in SerialEM, you can “save to other” under the file drop down menu, and select mrc as the format you want. This should work for you, just make sure that the map is loaded
 at full resolution in SerialEM, and not binned.
cheers
Garry




On Feb 6, 2026, at 5:35 AM, 蔡舒君 via 3dem <3dem at ncmir.ucsd.edu> wrote:




[External email - use caution]





Dear Colleagues, 



After collecting a map using SerialEM, the output file (map.mrc) contains multiple 2D images (e.g., 169 images with dimensions X × Y × Z = 1024 × 1024 × 1), along with the coordinate information for each image. When I open map.mrc in 3dmod, it appears
 as a single montage map (e.g., X × Y × Z = 12088 × 12088 × 1). 



Could you please advise on how to save this single montage map as a single MRC file (e.g., 12088 × 12088 × 1)?




Best regards,

Shujun













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