Difference between revisions of "Using thin spheres in DOCK3.7"

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==Tutorial for using Thin Spheres in DOCK 3.7==
 
==Tutorial for using Thin Spheres in DOCK 3.7==
  
written by Trent E. Balius, 2016/11/03.
+
Written by Trent E. Balius, 2016/11/03.
  
1) Run blastermaster.py.  this will generate two directories: working and dockfiles
+
1) Run blastermaster.py.  This will generate two directories: working and dockfiles
  
2) make a new directory called mk_thin_spheres:
+
2) Make a new directory called mk_thin_spheres:
 
   mkdir  mk_thin_spheres
 
   mkdir  mk_thin_spheres
 
   cd mk_thin_spheres
 
   cd mk_thin_spheres
  
3) First lets make a molecular surface.  We recommend that you make a less dense molecular surface by coping the rec.pdb and running the following command:
+
3) First lets make a molecular surface.  We recommend that you make a less dense molecular surface by copying the rec.pdb and running the following command:
 +
  cp ../rec.pdb .
 
   cp ../working/rec.site.dms .
 
   cp ../working/rec.site.dms .
 
   $DOCKBASE/proteins/dms/bin/dms rec.pdb -a -d 0.2 -i rec.site.dms -g dms.log -p -n -o rec.ms
 
   $DOCKBASE/proteins/dms/bin/dms rec.pdb -a -d 0.2 -i rec.site.dms -g dms.log -p -n -o rec.ms
  
Here, the -d flag allows us to pass the program a scaler to modify the density of the surface points.   
+
Here, the -d flag allows us to pass the program a scalar to modify the density of the surface points.   
for example, with a -d 1.0 the density is   5.42 pts/sq.A
+
For example, with a -d set to 1.0 the density is will be 5.42 pts/sq.A, while with a -d 0.2, we will get a density of 1.18 pts/sq.A.
while -d 0.2 we get a density of 1.18 pts/sq.A
+
  
Instead, you could copy the molecular surface the original surface (this is OK for small sites):
+
Instead, you could copy the molecular surface of the original surface (this is OK for small sites):
 
   cp ../working/rec.ms .
 
   cp ../working/rec.ms .
  
4) run thin sphere code:
+
4) Run the thin spheres code:
 
  /mnt/nfs/home/tbalius/zzz.svn/dockenv/trunk/etc/thin_spheres.py -i rec.ms -o delphi.sph >& thin_spheres.log
 
  /mnt/nfs/home/tbalius/zzz.svn/dockenv/trunk/etc/thin_spheres.py -i rec.ms -o delphi.sph >& thin_spheres.log
  
get the following python code:
+
Get the following python code:
 
  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/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/pdb_lib.py > pdb_lib.py
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     head delphi_close.sph
 
     head delphi_close.sph
  
if there are too mean sphere (> 1,000), decrease the distance to, say, 1.2.  
+
if there are too many spheres (> 1,000), decrease the distance to, say, 1.2.  
  
Note that this is avalible through the DOCK3.6 release.  
+
Note that this is available through the DOCK3.6 release.  
  
 
cd ../
 
cd ../
move back to the top dir.
+
move back to the top directory.
  
5) now lets setup dir and files to run blastermaster with Existing Low Dielectric Spheres
+
5) Now lets setup a directory and files to run blastermaster with the Existing Low Dielectric Spheres
 
make a new directory call dockprep_w_thin_sph/
 
make a new directory call dockprep_w_thin_sph/
 
     mkdir  dockprep_w_thin_sph
 
     mkdir  dockprep_w_thin_sph
Line 46: Line 46:
 
     cp ../../working/rec.crg.pdb working/.
 
     cp ../../working/rec.crg.pdb working/.
 
     cp ../mk_thin_spheres/delphi_close.sph working/lowdielectric.sph     
 
     cp ../mk_thin_spheres/delphi_close.sph working/lowdielectric.sph     
     # blaster master expect this to be cluster 1.  
+
 
 +
Make sure the header of the sphere file is cluster 1.
 +
     head working/lowdielectric.sph
 +
If it is not and says cluster 0 then run the following, because blaster master expects this to be cluster 1.  
 
     sed -i 's/cluster    0/cluster    1/g' working/lowdielectric.sph
 
     sed -i 's/cluster    0/cluster    1/g' working/lowdielectric.sph
  
 
6) Now lets run blastermaster with Existing Low Dielectric Spheres
 
6) Now lets run blastermaster with Existing Low Dielectric Spheres
 
     $DOCKBASE/proteins/blastermaster/blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag
 
     $DOCKBASE/proteins/blastermaster/blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag

Revision as of 12:05, 3 November 2016

Tutorial for using Thin Spheres in DOCK 3.7

Written by Trent E. Balius, 2016/11/03.

1) Run blastermaster.py. This will generate two directories: working and dockfiles

2) Make a new directory called mk_thin_spheres:

  mkdir  mk_thin_spheres
  cd mk_thin_spheres

3) First lets make a molecular surface. We recommend that you make a less dense molecular surface by copying the rec.pdb and running the following command:

  cp ../rec.pdb .
  cp ../working/rec.site.dms .
  $DOCKBASE/proteins/dms/bin/dms rec.pdb -a -d 0.2 -i rec.site.dms -g dms.log -p -n -o rec.ms

Here, the -d flag allows us to pass the program a scalar to modify the density of the surface points. For example, with a -d set to 1.0 the density is will be 5.42 pts/sq.A, while with a -d 0.2, we will get a density of 1.18 pts/sq.A.

Instead, you could copy the molecular surface of the original surface (this is OK for small sites):

  cp ../working/rec.ms .

4) Run the thin spheres code:

/mnt/nfs/home/tbalius/zzz.svn/dockenv/trunk/etc/thin_spheres.py -i rec.ms -o delphi.sph >& thin_spheres.log

Get the following python code:

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
   
   python close_sph.py delphi.sph ../xtal-lig.pdb delphi_close.sph 2.0
   head delphi_close.sph

if there are too many spheres (> 1,000), decrease the distance to, say, 1.2.

Note that this is available through the DOCK3.6 release.

cd ../ move back to the top directory.

5) Now lets setup a directory and files to run blastermaster with the Existing Low Dielectric Spheres make a new directory call dockprep_w_thin_sph/

   mkdir  dockprep_w_thin_sph
   cd dockprep_w_thin_sph
   cp ../rec.pdb ../xtal-lig.pdb .
   mkdir working
   cp ../../working/rec.crg.pdb working/.
   cp ../mk_thin_spheres/delphi_close.sph working/lowdielectric.sph    

Make sure the header of the sphere file is cluster 1.

   head working/lowdielectric.sph

If it is not and says cluster 0 then run the following, because blaster master expects this to be cluster 1.

   sed -i 's/cluster     0/cluster     1/g' working/lowdielectric.sph

6) Now lets run blastermaster with Existing Low Dielectric Spheres

   $DOCKBASE/proteins/blastermaster/blastermaster.py --useExistingLowDielectricSphflag --addNOhydrogensflag