Chemical Shift Input
[?] 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 POMONA & CS-RosettaCM, 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.    
Alignment Settings [+]
Modeling Options
[?] Select this option to generate a package of inputs for running a RosettaCM full atom modeling, which includes: RosettaCM scripts and required scoring files, de novo fragments (selected with chemical shifts), strucutre templates from Pomona alignments
Num. of Selected Top Clusters [?] Select this option to specify the number of top POMONA clusters selected to generate template inputs for CS-RosettaCM full atom modeling, with an allowed range of 1-100.
Num. of Alignments per Cluster [?] Select this option to specify the number of POMONA alignments per cluster selected to generate template inputs for CS-RosettaCM full atom modeling, with an allowed range of 1-100.
Note: attachments with large size (~20MB for 300-residue proteins) will be sent via email, make sure your email can receive such files!
Submission Details
[?] Calculation results will be sent via Email only. Email Address should not contain special characters.

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last update: Apr 6, 2015