| PDB Extended Structure: |
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Input PDB file with an extended structure of the protein.
This is used to establish amino acid
sequence and atom names. Atom names in the PDB file must exactly match the
the names used in the dipolar coupling input. Example: ubiq_ext.pdb
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Dipolar Coupling Input
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| Dipolar Coupling Input A: |
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Input table of dipolar couplings associated with one alignment medium.
The format of the input dipolar coupling table is described in the
DC Web Page. Example: dObsA.tab (Neutral Bicelle Sample)
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| Dipolar Coupling Input B: |
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Optional Input table of dipolar couplings associated with an alternate alignment medium.
The format of the input dipolar coupling table is described in the
DC Web Page. Example: dObsB.tab (Charged Bicelle Sample)
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| Dipolar Interaction Values: |
Keep Existing DI Values
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Select this option to use existing Dipolar Interaction (DI) values in the DC input tables.
Otherwise, DI values will be calculated according to information in the PDB file.
In the case of common fixed-geometry peptide couplings
(HN-N, HN-C ', N-C ', N-CA, CA - C ', H - CH3 and HA-CA)
standardized interatomic distances will be used to calculate DI. Otherwise,
atomic distances from the PDB file will be used. If a DI value of 0.0 is specified
in the input file, it will always be replaced with a DI value using atomic
distances from the PDB file.
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Optional Experimental Data
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| Shift Input: |
|
Optional input table of backbone chemical shifts. Use of chemical shifts can improve
the quality of MFR search results. The format of the table is the same
as for the TALOS+ software system.
Example: ubiq.tab
As an alternative, the input table of chemical shifts and
sequence information can be specified as a
BMRB NMR-Star format file.
In order to use NMR-Star format as input for MFR, 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.
Example: ubiq.str
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| J-Coupling Input: |
|
Optional input table of J-couplings for backbone torsions and their corresponding
Karplus parameters. Use of of such J-Coupling values can improve the quality of
MFR search results. Example: jcoup.tab
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Graphical Output
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| Graphical Output: |
Generate PDF Graphics
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Select this option to generate graphs of the MFR results in PDF format.
Example DC graphics for a protein:
dc.pdf Example DC graphics for a small molecule:
dcmol.pdf
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