Difference between revisions of "Using thin spheres in DOCK3.7"
From DISI
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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. | |
| − | 1) Run blastermaster.py. | + | 1) Run blastermaster.py. This will generate two directories: working and dockfiles |
| − | 2) | + | 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 | + | 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 | + | 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. | |
| − | 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) | + | 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: | |
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 | ||
| Line 31: | Line 31: | ||
head delphi_close.sph | head delphi_close.sph | ||
| − | if there are too | + | if there are too many spheres (> 1,000), decrease the distance to, say, 1.2. |
| − | Note that this is | + | Note that this is available through the DOCK3.6 release. |
cd ../ | cd ../ | ||
| − | move back to the top | + | move back to the top directory. |
| − | 5) | + | 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 | ||
| − | + | ||
| + | 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 11:05, 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
