How can I visualize the map online properly?

Please utilize the structural tools located on the right side of the visualization panel. Begin by clicking the "Show Map" button above to load the map. Next, click the ellipsis ("...") to the right of "Isosurface" within the volume section. Subsequently, click the ellipsis ("...") next to "Type" within the isosurface settings. Finally, adjust the iso-value to the appropriate values to visualize the map online.


What are the steps to submit a job in the EM Server?

You can view our tutorial at https://em.kiharalab.org/tutorial


How can I model a multi-chain complex by DeepMainmast (for proteins) and CryoREAD (DNA/RNA)?

Input all the sequences in the complex. If it has multiple copies of the same chain (homo-multimer), include the sequence exactly the number of times corresponding to the copies in the complex.


How do I submit a job?

In the top page, click a Method you like in the table. Or click "ALGORITHMS" and click the tool you would like to use.


Which paper should I cite if I used this server?

Please cite a paper of the method you used from this list: https://em.kiharalab.org/references


Who should I make contact with if I encounter problems?

Please check here for contact information: https://em.kiharalab.org/contact


Who can view the data I submit to the website? Can I submit my job confidentially?

The submitted data by you is not visible to other users. However, administrators at Kiharalab have technical access to this data, strictly for maintenance purposes. It is important to note that we will never release the submitted data outside the lab. For complete confidentiality while using our tools, you have option to either download the code or to use Google Colab Notebook. Links to these options are available at https://kiharalab.org/emsuites/.


How to prepare the fasta file in DAQ-Refine?

Please use a sequence file with fasta format. If the target protein has multiple chains, please put all sequences. Each chain must have a ID line (begin with a carat (">")) and a SEQUENCE line.

For ID line, please only include the chain id without any other information. If multiple chains include the identical sequences, please use comma "," to split different chains.

Example Sequence ID line
>A,B,C,D
MATPAGRRASETERLLTPNPGYGTQVGTSPAPTTPTEEEDLRR
>E,F
VVTFREENTIAFRHLFLLGYSDGSDDTFAAYTQEQLYQ

which indicates 6 chains with A,B,C,D share the identical sequences and E,F share another identical sequences.


How to prepare the pdb file in DAQ-Refine?

Please combine all single-chain structures in one PDB file, separated by "TER" for different chains' records. The chain ID does not matter, for identical chains, you only need to provide the chain records once in the pdb format.

Please make sure that the number of chains in the PDB file is smaller than the number of sequences in the sequence file.


What is the alignment strategy in DAQ-Refine? Which one should I choose?

Daq-refine would run a loop for all chains to finish the whole job. For each chain in the pdb file, it needs the cryo-em map and the fasta sequence as inputs. So deciding which sequence to run for some chain is crucial for the final results.

The alignment strategy here is how you choose to do this alignment job. If you choose the 'Mannual alignment', Daq-refine would do nothing just following the order in the input files to handle the job. If you choose 'Smith Waterman alignment',it would take the Smith Waterman algorithm to align the pdb file and the fasta file.

A simple tutorial for the mannual alignment is that if you download the sources files from the same Protein Bank, like RCSB. They usually have the key words for you to align.
For example, the protein 8g05_1 sequence in fasta file is

>8G05_1|Chain A[auth R]|G-protein coupled receptor 84|Homo sapiens (9606)
DYKDDDDHHHHHHHHGQPGNGSAFLLAPNGSHAPDHNVTQQRDEENL.............

The name for this chain is G-protein coupled receptor 84 from RCSB and it will be also marked in the PDB file, using this key,you can easily finish the mannual alignment thing.


Do I need to register? What is the benefits of registration?

No, registration is not mandatory. If you register, you can keep and retrieve your jobs on our system from the "My Jobs" tab. Additionally, we can contact you if your jobs have some problems providing suggestions for resolving the problems.


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