Scripts of the NMRPipe System
dynBasicExt.tcl: Create a Simple Extended Structure for a DYNAMO GMC Environment.
Usage:
dynBasicExt.tcl gmcDir outPDBName [args]
Input:
| Flag |
Argument |
Default |
Description |
-in |
inName |
gmcDir/random.pdb |
|
Output:
-print |
printCount |
10 |
Status Printing Interval. |
-report |
|
|
reportFlag List Final Atom Coord Info. |
-graph |
|
|
Graph Enregy Terms (Default). |
-nograph |
|
|
No Graphics. |
-reset |
|
|
Reset Seg Name of Output to Blank. |
-noreset |
|
|
Keep Seg Name of Output (Default). |
-rasmol |
rasmolFlag |
0 |
RasMol Drawing Interval. |
-wireframe |
|
|
Use RasMol Wireframe Mode. |
Annealing Options:
-tInit |
tInit |
4000 |
Annealing Temperature |
-initSteps |
initSteps |
1000 |
Initialization Step Count. |
-highSteps |
highSteps |
2000 |
High Temperature Step Count. |
-coolSteps |
coolSteps |
4000 |
Cooling Step Count. |
-vdw |
|
|
Use Van der Waals Term (Default). |
-novdw |
|
|
No Van der Waals Term. |
Backbone Angles (Protein Only):
-helix |
|
|
Reset Backbone Angles (Default). |
-nohelix |
|
|
Leave Backbone Angles Unchanged. |
-phi |
phiInit |
-64 |
Phi Angle for Backbone. |
-psi |
psiInit |
-41 |
Psi Angle for Backbone. |
|
|