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Submit a job to EMFF server!



The EMFF server uses a modified elastic network model (MENM) to flexibly fit a given initial protein structure into a given cryo-EM density map. The basic idea is to minimize a pseudo-energy which linearly combines various terms of the MENM energy (for pseudo-bonds, secondary structures and tertiary contacts) with a cryo-EM-fitting score and a collision energy that penalizes steric collisions(for details of the method see reference).

To run EMFF server, you need to upload the following two files and set several parameters:
Upload the PDB file for the initial structure (example)
Note: only records starting with the keyword "ATOM" will be considered. Your PDB file must be smaller than 2 MB, or else it will not be uploaded correctly!


Upload the EM map file to be fitted (example: X-PLOR format, 10Å resolution)
Please provide the following information about your EM map:
The format of your EM map file:
The resolution of your EM map (in Angstrom):
The grid unit (size of voxel edge) of your EM map if in SPIDER format (in Angstrom):
Note: the maximum size (number of voxels) of your EM map is 100*100*100, so please use a larger grid unit to reduce the EM map size if necessary.



Prior to the flexible fitting, the initial structure needs to be rigidly fitted into the given EM map. You can perform your own rigid fitting (and skip it here) or let the server do it for you. Please make your choice:



After the rigid fitting and before the flexible fitting, the EM map will be 'trimmed' to keep only voxels within certain buffer distance from the initial protein structure. The goal is to keep densities belonging to a single protein if multiple proteins are present in the EM map. If you want to use this option, please enter the value of buffer distance (in Angstrom):



To reduce the influence of solvent densities on fitting, the EM map should be 'clamped' by removing voxels with density value below certain threshold. Please enter the value of density threshold (default value is zero):



Optionally, you can upload the PDB file for the target structure for comparison with the EM-fitted models.
Upload the PDB file for the target structure (example)
Note: only records starting with the keyword "ATOM" will be considered. Your PDB file must be smaller than 2 MB, or else it will not be uploaded correctly!


Please enter a title for your job (it must be 4 alphanumeric characters). It will be used in the names of the output files.
job title

If you wish to be notified by email once your job is finished, please enter your e-mail address below (it will also allow us to send you diagnostic information in case your job fails). Otherwise you will be given a URL to your job outputs upon submission of your job, which you can check back later. Your e-mail address will be used only for the above purpose and then it will be discarded unless you choose to receive updates about this server.

E-mail

Click here if you wish to receive future updates about the AD-ENM server.





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