Emap2sec+

Emap2sec+ is a computational tool that can accurately identify structures, alpha helices, beta sheets, other(coils/turns) and DNA/RNA, in cryo-Electron Microscopy (EM) maps of medium to low resolution.

Input file:
    EM map file (mrc format file).
Parameter:
    Contour Level.   Please make sure your contour level is lower than your focused region. This is the absolute density threshold, not the standard deviation.

Result Visualization Panel:
Red indicates alpha helix, yellow indicates beta-strand, green indicates coil region of proteins, and purple indicates DNA/RNA.

Output Logs Panel:
The "Output Logs" panel include all the outputs from the scripts. If you are interested in the progress of the job during running, you can take a look at it.

Job Configuration Panel:
The "Job Configuration" panel includes the input parameters for this job, which is used to keep the records of your submitted input.

Problem Debugging:
If you encounter any problems, feel free to email us to report the problems. In your email, please use subject as "Emap2sec+ problem: [jobid]", here [jobid] is the job is shown in the title. We will use the jobid to locate and debug jobs in the backend and get back to you as soon as possible.

Contact:
dkihara@purdue.edu, gterashi@purdue.edu, xiaowang20140001@gmail.com.

Emap2sec+ is a computational tool that can accurately identify structures, alpha helices, beta sheets, other(coils/turns) and DNA/RNA, in cryo-Electron Microscopy (EM) maps of medium to low resolution.

If encounter problems, please contact Daisuke Kihara (dkihara@purdue.edu) or Xiao Wang (xiaowang20140001@gmail.com)


Example EMD-7103
Input Map file:7103.mrc

Contour level: 0.006

Result Example:Result Example
Tutorial.

Reference: https://www.nature.com/articles/s41467-021-22577-3


Please simply click "Schedule Job" when you filled all input fields.

Please make sure your contour level is lower than your focused region. This is absolute density threshold, not standard deviation.

Please input valid contour level since it is used for normalization in Emap2sec+. 0 is not suggested and may ruin the visualization..