Calculate volume of the binding site and molecules - Revision history

TBalius at 18:51, 6 February 2019

2019-02-06T18:51:58Z

← Older revision		Revision as of 18:51, 6 February 2019
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	* Calculate the volume using the following script: [http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]		* Calculate the volume using the following script: [http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]

			==Calculating the volume of a binding site using scripts==



	== Calculating the volume of a small molecule. ==		== Calculating the volume of a small molecule. ==

TBalius: /* Calculating the volume of a binding site. */

2019-01-24T01:29:48Z

Calculating the volume of a binding site.

← Older revision		Revision as of 01:29, 24 January 2019
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	*This file should contain:		*This file should contain:
	**specifies the input file		**specifies the input file
	**spheres generated will be outside of ~~teh~~ receptor surface		**spheres generated will be outside of the receptor surface with R and inside with L
	**specifies that all points ~~won~~ the receptor will be used		**specifies that all points on the receptor will be used
	**distance in angstroms (avoids steric clashes)		**distance in angstroms (0.0 avoids steric clashes), try -0.1 to completely fill the site, but some clashes.
	**max surface radius of the spheres in angstroms		**max surface radius of the spheres in angstroms
	**min surface radius of the spheres in angstroms		**min surface radius of the spheres in angstroms

Jyoung: /* Calculating the volume of a binding site. */

2018-10-10T18:35:06Z

Calculating the volume of a binding site.

← Older revision		Revision as of 18:35, 10 October 2018
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	rec.sph contains the spheres		rec.sph contains the spheres

	Information ~~modifed~~ from [http://ringo.ams.sunysb.edu/index.php/2016_DOCK_tutorial_with_Beta_Trypsin#Creating_Spheres rizzo group wiki]		Information modified from [http://ringo.ams.sunysb.edu/index.php/2016_DOCK_tutorial_with_Beta_Trypsin#Creating_Spheres rizzo group wiki]

	* Select the cluster that defines the binding site of interest by visualization in Chimera.		* Select the cluster that defines the binding site of interest by visualization in Chimera.

Jyoung at 17:08, 10 October 2018

2018-10-10T17:08:11Z

← Older revision		Revision as of 17:08, 10 October 2018
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	~~Alternavively~~, this command will find all ligands close to your the ligand.		Alternatively, this command will find all ligands close to your the ligand.
	python close_sph.py all_spheres.sph ../xtal-lig.pdb delphi_close.sph 2.0		python close_sph.py all_spheres.sph ../xtal-lig.pdb delphi_close.sph 2.0
	head delphi_close.sph		head delphi_close.sph

TBalius at 18:28, 14 September 2018

2018-09-14T18:28:19Z

← Older revision		Revision as of 18:28, 14 September 2018
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	Written by Trent Balius, Dec. 2016.		Written by Trent Balius, Dec. 2016.

	The method and scripts discribed here was usied in ~~the following~~ paper		The method and scripts discribed here was usied in this paper
	[https://pubs.acs.org/doi/10.1021/acschembio.8b00443].		[https://pubs.acs.org/doi/10.1021/acschembio.8b00443].

TBalius at 18:26, 14 September 2018

2018-09-14T18:26:21Z

← Older revision		Revision as of 18:26, 14 September 2018
Line 3:		Line 3:

	The method and scripts discribed here was usied in the following paper		The method and scripts discribed here was usied in the following paper
	[[https://pubs.acs.org/doi/10.1021/acschembio.8b00443]].		[https://pubs.acs.org/doi/10.1021/acschembio.8b00443].

	The script to calculate volume is available here: [http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]		The script to calculate volume is available here: [http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]

TBalius at 18:26, 14 September 2018

2018-09-14T18:26:01Z

← Older revision		Revision as of 18:26, 14 September 2018
Line 1:		Line 1:

	Written by Trent Balius, Dec. 2016.		Written by Trent Balius, Dec. 2016.

			The method and scripts discribed here was usied in the following paper
			[[https://pubs.acs.org/doi/10.1021/acschembio.8b00443]].

	The script to calculate volume is available here: [http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]		The script to calculate volume is available here: [http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]

TBalius at 01:59, 7 December 2016

2016-12-07T01:59:40Z

← Older revision		Revision as of 01:59, 7 December 2016
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	Run the python program as follows:		Run the python program as follows:
	>> python ~/zzz.scripts/volume_cal_sph.py lowdielectric_mod.sph 0.5 out		>> python ~/zzz.scripts/volume_cal_sph.py lowdielectric_mod.sph 0.5 out
			Here is the output:
	input file = lowdielectric_mod.sph		input file = lowdielectric_mod.sph
	scale = 0.5		scale = 0.5

TBalius at 01:58, 7 December 2016

2016-12-07T01:58:15Z

@@ Line 12: / Line 12: @@
   curl http://docking.org/~tbalius/code/for_dock_3.7/mol2.py > mol2.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/mol2toSPH_radius.py > mol2toSPH_radius.py
 ==how the volume calculation works.==
@@ Line 28: / Line 31: @@
 ==Calculating the volume of a binding site.==
-You can run blastermaster.py which is distributed with DOCK3.7 and then use the lowdielectric.sph to define the pocket.
+You can run blastermaster.py which is distributed with DOCK3.7 and then use the all_spheres.sph or lowdielectric.sph to define the pocket.
   mkdir cal_vol
   cp ../working/lowdielectric.sph .
 You should visualize these sphere in UCSF Chimera to make sure that they file the site and do not go outside [[DOCK_3.7_2014/09/25_FXa_Tutorial#Receptor_Preparation]].
-If they do use a text editor to remove the necessary spheres or add new ones.
+If they do you can use a text editor to remove the necessary spheres or add new ones.
 Run the python program as follows:
@@ Line 53: / Line 65: @@
 * run dms (or you can also generated the molecular surface with Chimera) to generate a molecular surface.
+  $DOCKBASE/proteins/dms/bin/dms rec.pdb -a -g dms.log -p -n -o rec.ms
 * Use the sphgen program(distributed with all versions of DOCK) to flood the surface of the protein with spheres, which are then cluster by distance.
 * Select the cluster that defines the binding site of interest by visualization in Chimera.
-* Copy the sphere file. Using a text editor (vim) remove all clusters except the one of interest.
+** Copy the sphere file. Using a text editor (vim) remove all clusters except the one of interest. (or see above for script that does this).
 * Calculate the volume using the following script: [http://docking.org/~tbalius/code/for_dock_3.7/volume_cal_sph.py volume_cal_sph.py]

TBalius at 22:31, 4 December 2016

2016-12-04T22:31:34Z

← Older revision		Revision as of 22:31, 4 December 2016
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	If they do use a text editor to remove the necessary spheres or add new ones.		If they do use a text editor to remove the necessary spheres or add new ones.

	python ~/zzz.scripts/volume_cal_sph.py lowdielectric_mod.sph 0.5 out		Run the python program as follows:
			>> python ~/zzz.scripts/volume_cal_sph.py lowdielectric_mod.sph 0.5 out
	input file = lowdielectric_mod.sph		input file = lowdielectric_mod.sph
	scale = 0.5		scale = 0.5
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	molN= 1092 boxN= 5610 boxV= 701.25		molN= 1092 boxN= 5610 boxV= 701.25
	molV= 136.5		molV= 136.5

			This script also produces a dx file so that you can visualize (in chimera) the points which are overlapping with the spheres.