There are multiple terms or items that are displayed on our interface that are not totally clear on how what they mean to someone who isn't well informed.
Format of following suggestions:
* Item/Term to receive tooltip
* Suggested location
* Suggested content, in quotes
* Context of suggestion (why its needed)
Terms
RMSD
Details panel next to RMSD attribute & inside of popup for filter
"Stands for Root-mean-square deviation of atomic positions.\nA lower RMSD indicates a better alignment"
Using this for the first time or finding it online isn't going to have all of the context necessary to benefit from what this important number actually means, like someone in a classroom environment might be given.
Search Form
EC Class
Next to form element
"Default: none.\nFilter the motifs to only those with a certain EC Class. There are a few motifs with an unknown EC Class and they will always be included in the results."
Clarify action taken by filling this out
Precision
Next to form element
"Default: 1. Requirements: Must be positive.\nIncreasing the precision factor increases the acceptable distance between a set of atoms when doing an alignment."
Clarify action taken by filling out element
Custom Structure
Next to the button (or on hover)
"Supports PDB or MMCIF files.\nUpload a custom structure to be included in the alignment. The PDB id will be parsed out of the structure to be included in the response. A custom structure will be listed with any motifs we were able to match to it."
Set expectations as to what this does
Custom Motif
Next to the button (or on hover)
"Supports MOTIF files.\nCompare custom motifs with PDB structures inputted, as well as any custom structures uploaded. We will list for every query structure if a custom motif found an alignment, or if it did not."
Maker Form
Motif Structure [This form element needs a title]
To the right the title, which would be just above "Standard" / "Custom" toggle
"If the protein you are using is available in the RCSB's database we can obtain the structure directly from them. Otherwise, we will need you to provide the structure by selecting "Custom" and uploading the correct PDB or MMCIF file."
Its currently unclear what this selection is doing to someone naive to the process.
Motif Structure "Standard" EC Class
To the right of the form element
"This is used for finding the protein's homologs. If it is not known, please leave blank and we will set it to 'unknown' in the created motif, we will not be able to run a homolog test, however, you can still compare to a custom list using the List test option and inputting PDB ids."
The EC number might not be always known and so we need to make sure that we are clarifying to the user what will happen if they do not include it.
Active Site Residues [SECTION NAME CHANGE: there is only one active site, but there are multiple residues]
To the right of the section header.
"List the residues in the active site, minimum three.\nIf there are alternate positions available in the structure for a residue in the active site, please do not indicate an option. At the time of alignment, we will identify the alternative positions and compare them with the structure to find the best alignment."
Clarify that there is a hard minimum of three residues so that people are not surprised by an error if they list only two. And clarify that entering alternate position information is not needed.
Custom Structures
To the right of the button
"Supports PDB and MMCIF. Include custom structures in your test. These are tested alongside any of the test options selected. The PDB id will be parsed from the structure file and will be the identifier when returned."
This clarifies that custom structures will be run along with any test request.
Test Options
(These are to set appropriate expectations for the user about what each option does)
Self
"Test the above motif against its own structure. If it does not find an alignment, there is likely a typo in the entered residues."
Homolog
"Test the above motif against all proteins with the same EC Class, as defined by the PDB."
Random
"Test the above motif against a number of randomly selected proteins from the PDB."
List
"Test the above motif against a list of proteins available on the PDB."
There are multiple terms or items that are displayed on our interface that are not totally clear on how what they mean to someone who isn't well informed.
Format of following suggestions:
Terms
\nA lower RMSD indicates a better alignment"Search Form
\nFilter the motifs to only those with a certain EC Class. There are a few motifs with an unknown EC Class and they will always be included in the results."\nIncreasing the precision factor increases the acceptable distance between a set of atoms when doing an alignment."\nUpload a custom structure to be included in the alignment. The PDB id will be parsed out of the structure to be included in the response. A custom structure will be listed with any motifs we were able to match to it."\nCompare custom motifs with PDB structures inputted, as well as any custom structures uploaded. We will list for every query structure if a custom motif found an alignment, or if it did not."Maker Form
[This form element needs a title][SECTION NAME CHANGE: there is only one active site, but there are multiple residues]\nIf there are alternate positions available in the structure for a residue in the active site, please do not indicate an option. At the time of alignment, we will identify the alternative positions and compare them with the structure to find the best alignment."Test Options
(These are to set appropriate expectations for the user about what each option does)