Chemical Shift Input
      [Allowed format] The input table of chemical shifts and sequence information. The format of the table is described in the TALOS Web Page.

As an alternative, the input table of chemical shifts and sequence information can be specified as a BMRB NMR-Star format (v2.1 or v3.1) file.

In order to use NMRSTAR format as input to CS-Rosetta, the BMRB file should have chemical shift information and complete sequence information for a single protein only. When input is supplied as a BMRB file, CYS residues with a CB shift of 34ppm or less are assumed to be reduced, and HIS residues in tables with a listed pH of 6.0 or less are assumed to be protonated.

Referencing Offset Select this option to test the input chemical shift referencing and apply an automated offset correction if needed. Deuterium Effect Deuterium Correction (Deuterated Proteins Only). Select this option if the input CA and CB chemical shifts need to be adjusted for deuterium isotope effect. Leave this option off if you have already adjusted the CA and CB shifts.
Automatic Select this option to automatically identify and trim flexible talis by using a RCI-S2 cutoff of 0.65.

Warning: All tail resisdues without chemical shift assignments will be assigned as flexible by this automatic procedure. If it is not the fact, users can use the other option to manually specify the flexible residues. 		Selected Residues Use this option to specify the flexible residues to be trimmed, with a separator of a space character.    
Fragment Searching Settings
Max. Allowed Sequence Identity Specify in this option the sequence identity value if sequence homologues in the database need to be excluded, with an allowed range of 0.0-100.0 %
Excluded PDB Specify in this option the proteins that need to be excluded, all proteins should be listed by a seperator of a space and with a format of 4-letter PDB identifier plus a 1-letter chain id, such as:

1ubqA 1d3zA 2oedA
[+] more options ..
Output Options
Standard CS-Rosetta Select this option to generate a package of inputs for running a CS-Rosetta full atom modeling, which includes: Rosetta3.x script and flag file, de novo fragments (selected with chemical shifts), Rosetta model evaluation script Fold_Dock CS-Rosetta Select this option to generate a package of inputs for running a CS-Rosetta full atom modeling, which includes: Rosetta3.x script and flag file, de novo fragments (selected with chemical shifts), Rosetta model evaluation script SymDock CS-Rosetta Select this option to generate a package of inputs for running a CS-Rosetta full atom modeling, which includes: Rosetta3.x script and flag file, de novo fragments (selected with chemical shifts), Rosetta model evaluation script
NOE constraint Select this option to generate a package of xxx
RDC constraint (medium 1) Select this option to generate a package of inputs for running a CS-Rosetta full atom modeling xxx [+]
RDC constraint (medium 2) Select this option to generate a package of inputs for running a CS-Rosetta full atom modeling xxx [×]
RDC constraint (medium 3) Select this option to generate a package of inputs for running a CS-Rosetta full atom modeling xxx [×]
Submission Details
[?] Calculation results will be sent via Email only. Email Address should not contain special characters.

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last update: July 31, 2014