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Frank
Delaglio, Ph.D.
Software Science Consultant
13840 Grey Colt Drive
North Potomac MD 20878 USA
Tel: 301 806-0867
Fax: 301 309-8717
E-mail: delaglio@nmrscience.com
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Scripts of the NMRPipe System
talos.tcl: predicts angles from chemical shift homology.
Directory Settings:
| Flag |
Argument |
Default |
Description |
-talosDir |
mDir |
. |
TALOS Main Directory: TALOS_DIR. |
-shiftDir |
sDir |
shifts |
Subdirectory of master shifts. |
-pdbDir |
pDir |
pdb |
Subdirectory of master structures. |
-tabDir |
tDir |
tab |
Subdirectory of master tables. |
-predDir |
pDir |
pred |
Directory for prediction results. |
File Name Settings:
-in |
inName |
None |
Input Shift Table. |
-sum |
sumName |
pred.tab |
Prediction Summary Output. |
-homo |
hName |
homology.tab |
Residue Homology Table. |
-map |
mName |
vina.dat |
Ramachandran Map Name. |
-db |
dbName |
talos.tab |
TALOS triplet database file. |
-w |
wName |
weight.tab |
TALOS triplet weighting file. |
Random Coil and Secondary Shift Tables:
-rand |
rName |
randcoil.tab |
Random Coil Shift Table. |
-adj |
aName |
rcadj.tab |
Adjustment Table. (None for no adjustment). |
-prev |
pName |
rcprev.tab |
Previous Residue Adjustment. (None for no adjustment). |
-next |
nName |
rcnext.tab |
Next Residue Adjustment. (None for no adjustment). |
-limits |
lName |
sslimit.tab |
Secondary Shift Limits. (Used only with -clip). |
Other Options:
-excl |
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eList List of Proteins to Exclude. |
-first |
resID1 |
First |
First RESID to use. |
-last |
resIDN |
Last |
Last RESID to use. |
-thresh |
tVal |
200.0 |
Max Distance Threshold. |
-count |
mc |
10 |
Max Match Count per Triplet. |
-clip |
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Clip Extreme Shifts (Default). |
-noclip |
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No Clipping of Shifts. |
-compile |
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Re-compile triplet database. |
Allowable Percentage of Undefined Shifts
-dbpct |
defPct |
59.0 |
Minimum, Database Triplet. |
-tpct |
tPct |
15.0 |
Minimum, Target Triplet. |
Special Fast-Mode Searching (Only Availble on Some Systems):
-fast |
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Use Fast Mode When Available (Default). |
-nofast |
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Use Ordinary TCL-Based Search. |
-sleep |
sTime |
5 |
Sleep Time After Fast Mode Search, Sec. |
Examples:
talos.tcl -in ubiq.tab Form predictions from the given shifts.
talos.tcl -compile Re-compile the triplet database.
See Also:
vina.tcl Summarize predictions in a single table.
rama.tcl Graphical interface to inspect results.
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last updated: Apr 20, 2011 / big frank
Contact site designer mimi at
mdelaglio@hotmail.com
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