Resonance Assignment/Abacus/FMCGUI objects: Difference between revisions
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==== Typing probabilities ==== | ==== Typing probabilities ==== | ||
| <span>T<sup>t </sup>(f) </span><span>is a probability for fragment ''f ''to have amino acid type ''t''</span><span>. Here ''t ''corresponds to one of 20 amino acid residue types, and f </span><span>is fragment user ID. </span> | ||
<span>Typing probbilities could be calculated or modified manually by the commands {[[Fragment>Type>Calculate]]} and {[[Fragment>Type>Fix]]}, respectively.</span> | |||
=== Contact map === | === Contact map === |
Revision as of 20:31, 30 November 2009
- protein sequence
- peak list
- and PB fragments.
Protein sequence
Peak list
- (+) peak list is required to be referenced
- (+/-) peak lists could be referenced optionally
- (-) peak lists for which referencing is not used even if it is present in the input file
N15 NOESY
|
-
|
C13 NOESY H2O
|
-
|
Arom NOESY
|
-
|
N15 HSQC
|
+
|
C13 HSQC
|
+
|
HNCA
|
+/-
|
HNCO
|
-
|
CBCACONH
|
+/-
|
HBHACONH
|
+
|
List of PB fragments
User ID
Fragment ID assigned by user, U_id. U_id can’t be changed within FMCGUI.
Assignment ID
Assignment ID, A_id, indicates the sequence position ID to which the fragment is assigned.
A_id = -99 if the fragment is not assigned to any position in the sequence.
A_id could be set up or modified by the following commands: { [[FMCGUI commands>Assignment>Fix Assignment>Manually|Assignment>Fix Assignment>Manually]] }, { [[FMCGUI commands>Assignment>Fix Assignment>Using Probability map|Assignment>Fix Assignment>Using probability Map]] }, and { [[FMCGUI commands>Assignment>Fix Assignment>Reset all|Assignment>Fix Assignment>Reset all]] }.
Typing probabilities
Tt (f) is a probability for fragment f to have amino acid type t. Here t corresponds to one of 20 amino acid residue types, and f is fragment user ID.
Typing probbilities could be calculated or modified manually by the commands {[[Fragment>Type>Calculate]]} and {[[Fragment>Type>Fix]]}, respectively.
Contact map
- Each fragment has three Fragment contact maps: , , and , respectively. Each contact map scores the possibility for any fragment f to be next to fragment U_id in the protein sequence; were f and U_id stand for fragment user ID.
Assignment probabilities
- FragmentFragment assignment probabilities and are calculated using SA and REM Monte Carlo simulations, respectively. Here s stands for protein sequence position ID.