The EMReady Web Server is an automatic post-processing web server for 3D cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) density maps using a deep learning-based framework. Users are required to provide an EM or ET density map in MRC2014 format with optionally mask structure file in PDB or CIF format. EMReady supports 3D cryo-EM and cryo-ET density maps within the resolution range of 2.0-10.0 Å. If you have any question or suggestion about EMReady Web Server, don't hesitate to contact us at the first time.
The maximum size of the uploading MRC file is limited to 500 Mb. After the user-specified EM density map is uploaded, NGL Viewer is used to display the input EM density map, where users can adjust the contour level.
Users can select the EMReady version between EMReady (version 1) and EMReady 2 (version 2), Generally, EMReady is better for protein-only maps at higherresolutions, while EMReady2 performs better for nucleic acid maps or intermediate-resolution maps. Users may aso try both.
Users can modify their EMReady job by changing the advanced settings:
Mask structure is used to ensure that EMReady optimizes only specific regions of the density map.
By default, no structure is used and EMReady improves the entire 3D density map.
Mask structure will enable EMReady to automatically generate masks around atoms.
If you want to improve the entire 3D density map, just don't input any mask structure.
Mask Radius is used to control the region of the mask generated by EMReady around the mask structure.
By default, the "4.0 Å" is used.
You can adjust the mask radius size according to your needs. Usually, 4.0 Å is a suitable option. The mask radius is effective only when a mask structure is provided.
Users can provide their email address to the EMReady server. Once the submitted job is finished, the users will be notified by a reminder email. The name of submitted jobs can also be specified by users.
After clicking the Start EMReady button, the job will be submitted to the server. Since the EM map file often have a large size, the job submission may take sometime. After the job is successfully submitted, the page will be redirected to the job status page. At this time, users may bookmark the page and access the results at a later time. The job status page will automatically refresh every 10s to show the job runing process. There are two job statuses for a successful submission, PENDING or RUNNING. A PENDING job means that it has been successfully submitted to the job system and temporarily waiting for resources. If the web server is down for regular maintenance, the submitted job will also be in PENDING status and the job will be scheduled to run once the server is up. A RUNNING job means that it has be allocated computing resources and is running on the server. After the job is finished, the job status page will turn to job result page. If users provided a valid email address, they may also receive an email notifying the job completion.
After an EMReady job is completed, the EMReady Web Server provides users a web interface to interactively view the processed map via NGL Viewer. The EMReady server provides results for download: processed maps.