Using thin spheres in DOCK3.7: Difference between revisions

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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
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     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 19:05, 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