November 17, 2022

TopFrag: Frag Code Descriptions Added to Script

When a user creates a new script using Generate FragCode Script in the ellipses menu of a saved structure, the Edit Script window now displays descriptions for each FragCode used as a list of non-executable code below the script:

• There are two blank lines of space between the bottom of the script and the top of the header for the code descriptions:
  • The header is in a line by itself and reads "FragCode Descriptions".
  • The code descriptions begin in a new line directly below the header.
• The codes are sorted in an ordered list with the description of that code following:
  • There is a "space-dash-space" that separates the code and the appropriate description. Example: \* H721 - 1 UNCONJUGATED ACYCLIC C=C (excludes exo bonds).
  • The sorting order is determined by the starting letter and then by the following number: A → Z and then 1 →100 → 200 → and so on. Example: D1, D2, D3....E511, E512, E513.
  • Codes M0, M2, M3, M4 do not require code descriptions and are omitted from the list.
  • Each code begins a new line in the script.
  • If a code is associated with a discontinued code, the discontinued code appears enclosed in parentheses directly next to the associated code. Example: \* K221(K220) - ORGANIC S-S-(S)n GROUP (n>1)
    
    

Biosequence Search Result Limit Parameter Removed

This release removes the Limit Total Sequence Results parameter from BLAST, CDR, and Motif sequence searches. Previously, the maximum number of sequence results returned was 20,000; now, the limit for all searches is 100,000.

Before

After

File Import Window Redesign

Previously, the user would see an Overwrite File window when they attempted to import/save a sequence, script, or structure with a file name the same as an existing file on the respective My Files page.

With this release, the Overwrite File functionality exists within the Import (File Type) window. The user now sees “File name already exists in this location” messaging with renamed action buttons:

• Importing/saving single file:
  • Replace (formerly Yes): Existing file overwritten with the new one.
  • Rename: User prompted to rename the new file before import/save.
  • Cancel or X: Dismisses Import window with no further actions and the file is not uploaded to the system.
    
    
    
    
• Importing multiple files at one time:
  • If the user has only one file that needs to be managed (replaced or renamed), the same buttons are present as if the user had uploaded a single file.
  • If the user has two or more files that need to be managed:
    • Replace All (formerly Yes to All): All new files waiting to be managed overwrite the appropriate existing files.
    • Replace and Rename: Same functionality stated above and then the next file to be managed displays.
    • Skip: Currently displayed file not uploaded to the system.
    • Cancel or X button: Any choices made for previous files are implemented and the Import window closes with no further actions. Any files left unmanaged will not be uploaded to the system.