POMONA/CS-RosettaCM Server | Bax Group NMR Calculation Servers at the NIH

Chemical Shift Input
Upload a Chemical Shift File

Chemical Shift 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 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.

[Input Examples]

Apply Corrections

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.

Trim Flexible Tails

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.

Choose Search Set Database

All PDB Proteins Select this option to search all proteins in PDB	Selected PDB Protein(s) Select this option to specify the protein(s) to be aligned. Proteins should be listed with a seperator of a space character and with a format of 4-letter PDB identifier plus a 1-letter chain id, such as: 1ubqA 1d3zA 2oedA

Exclusion Options

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

Alignment Settings [+]
Click [+] to view or change the default settings. Note that the default alignment settings will fulfill the needs of most users

Modeling Options
Generate CS-RosettaCM Inputs

[?] 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

Template Selection Options

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
Email

[?] Calculation results will be sent via Email only. Email Address should not contain special characters.

Confirm Email

By using this server you are agreeing to the Terms of Use.

Get the free Adobe Acrobat Reader application to view PDF files.

[ NMR Servers ] [ Home ] [ NIH ] [ NIDDK ]
last update: Apr 6, 2015