Difference between revisions of "How to do parameter scanning"

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(Created page with "Written by Jiankun Lyu, 2017/01/18 The hierarchy of the directory: thin_spheres_parameter_scanning----- std_dockprep ------ dockfiles | ...")
 
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Written by Jiankun Lyu, 2017/01/18
 
Written by Jiankun Lyu, 2017/01/18
  
The hierarchy of the directory:
+
The hierarchy of the directories:
  
 
  thin_spheres_parameter_scanning----- std_dockprep ------ dockfiles
 
  thin_spheres_parameter_scanning----- std_dockprep ------ dockfiles
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               ------- script ------ dockprep_thin_spheres_in_batches.csh
 
               ------- script ------ dockprep_thin_spheres_in_batches.csh
 
                               |
 
                               |
                               |----- submit_dockprep_change_sphere_size.csh
+
                               |------ submit_dockprep_change_sphere_size.csh
 
                               |
 
                               |
 
                               |------ dockprep_thin_spheres.csh
 
                               |------ dockprep_thin_spheres.csh
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                               ------- close_sph.py
 
                               ------- close_sph.py
  
1) Run blastermaster.py in std_dockprep.  This will generate two directories: working and dockfiles
+
1) Make those directories above.
 +
mkdir thin_spheres_parameter_scanning
 +
cd thin_spheres_parameter_scanning
 +
mkdir std_dockprep
 +
mkdir script
 +
 
 +
2) Run blastermaster.py in std_dockprep.  This will generate two directories: working and dockfiles
 +
 
 +
3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory
 +
cd script
 +
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
 +
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
 +
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py
 +
 
 +
4) Copy scripts from my path.
 +
cd script
 +
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
 +
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_change_sphere_size.csh .
 +
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .
 +
 
 +
5) Run parameter scanning.
 +
csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep
 +
 
 +
6) Submit enrichment calculation.

Revision as of 00:26, 19 January 2017

Written by Jiankun Lyu, 2017/01/18

The hierarchy of the directories:

thin_spheres_parameter_scanning----- std_dockprep ------ dockfiles
              |                            | 
              |                            |----- working
              |                            |
              |                            ------ other files generated balstermaster.py
              |
              ------- script ------ dockprep_thin_spheres_in_batches.csh
                              |
                              |------ submit_dockprep_change_sphere_size.csh
                              |
                              |------ dockprep_thin_spheres.csh
                              |
                              |------ sph_lib.py
                              |
                              |------ pdb_lib.py
                              |
                              ------- close_sph.py

1) Make those directories above.

mkdir thin_spheres_parameter_scanning
cd thin_spheres_parameter_scanning
mkdir std_dockprep
mkdir script

2) Run blastermaster.py in std_dockprep. This will generate two directories: working and dockfiles

3) Download sph_lib.py, pdb_lib.py and close_sph.py files into the script directory

cd script
curl http://docking.org/~tbalius/code/for_dock_3.7/sph_lib.py > sph_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/pdb_lib.py > pdb_lib.py
curl http://docking.org/~tbalius/code/for_dock_3.7/close_sph.py > close_sph.py

4) Copy scripts from my path.

cd script
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres_in_batches.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/submit_dockprep_change_sphere_size.csh .
cp /mnt/nfs/work/jklyu/AmpC/script/dockprep_thin_spheres.csh .

5) Run parameter scanning.

csh /path/to/script/dockprep_thin_spheres_in_batches.csh /path/to/script/ /path/to/std_dockprep

6) Submit enrichment calculation.