DistancesRH - Revision history

Bell: 1 revision

2014-05-26T23:33:24Z

1 revision

2014-05-22T16:56:10Z

download link and license update

2014-03-28T01:43:46Z

8 revisions

2013-01-13T15:39:01Z

2013-01-13T15:38:17Z

graphical outputs

2013-01-13T15:15:35Z

code update

2013-01-11T11:50:01Z

2013-01-11T11:49:25Z

code update

2013-01-04T11:45:48Z

2013-01-02T16:32:05Z

@@ Line 1: / Line 1: @@
 {{Infobox script-repo
 |type      = script
-|download  =
+|download  = [http://dx.doi.org/10.6084/m9.figshare.1031580 figshare]
 |author    = [[User:PietroGattiLafranconi|Pietro Gatti-Lafranconi]]
-|license   = [http://creativecommons.org/licenses/by-nc-sa/3.0 CC BY-NC-SA]
+|license   = [http://creativecommons.org/licenses/by/4.0/ CC BY 4.0]
 }}

@@ Line 63: / Line 63: @@
 Distances will now be calculated between atoms that can form H bonds only (figure 2, right).
-[[File:distancesRH_ex2.png|300px|example #2]]
+[[File:distancesRH_ex2.png|450px|example #2]]
@@ Line 72: / Line 72: @@
 Distances between atom NE2 of residue 19 in chain B of 1EFA and all atoms within 4.7 Å (all of which are in the DNA fragment of chain D, figure 3).
-[[File:distancesRH_ex3.png|450px|example #3]]
+[[File:distancesRH_ex3.png|300px|example #3]]

@@ Line 40: / Line 40: @@
 == Examples ==
-example #1
+'''example #1'''
 <source lang="python">
-distancesRH 2WHH, 25, 3.2
+distancesRH 2WHH, 25, 3.2, show=Y
 </source>
-Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen.
+Will show distances between all atoms of residue 25 in 2WHH and any atom within 3.2 Å and return the result on screen (figure 1, left).
-example #2
+'''example #2'''
 <source lang="python">
-distancesRH 1LVM, 151, 3, B, P, Y, Y, N
+distancesRH 1EFA, 901, 3.5, show=Y, Hbonds=Y
 </source>
-Will show distances between N of residue 151 in chain B of 1LVM and all atoms within 3 Å. Distances are limited to atoms that can form hydrogen bonds and will be printed in "dist_rH_151_N.txt". Dist objects will be shown in pymol.
+Distances will now be calculated between atoms that can form H bonds only (figure 2, right).

@@ Line 60: / Line 60: @@
 == Updates ==
-* '''11/01/2013''' - edit #1: ''distances are now calculated across different chains as well''
+* '''11/01/2013''' - edit #1: ''distances measured between different chains''
@@ Line 179: / Line 180: @@
 		print screenOP
 	if output=="P":
 		print 'data printed in "distances_rH_'+ref+'-'+aname+'.txt" file'
 		f=open('distances_rH_'+ref+'-'+aname+'.txt','w')

← Older revision		Revision as of 11:50, 11 January 2013
Line 60:		Line 60:

	== Updates ==		== Updates ==
−	* ''11/01/2013'' - edit #1: '''distances are now calculated across different chains as well'''	+	* '''11/01/2013''' - edit #1: ''distances are now calculated across different chains as well''

← Older revision	Revision as of 23:33, 26 May 2014
(No difference)

← Older revision	Revision as of 01:43, 28 March 2014
(No difference)

@@ Line 55: / Line 55: @@
 == Notes, Further Developments and Requests ==
-* This script works with visible objects
+* This script works with visible objects (handling of multiple states will hopefully be implemented soon)
 * As it is intended to be user-friendly more than fast, this script is not suitable to calculate distances between large objects. Use [[Quick_dist]] instead.
-* '''request #1''': a version that handles multiple states
 == The Code ==
 <source lang="python">
 from pymol import cmd, stored, math
@@ Line 94: / Line 117: @@
 		cmd.select("RefAtom", cen+refA)
 		m1=cmd.get_model ("RefAtom")
-	cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+cen)
+	cmd.select("Atoms", cen+refA+" around "+str(dist)+" and not resi "+ref+" and "+obj)
 	cmd.show("nb_spheres", "(Atoms or Reference) and (resn HOH or HET)")
 	cmd.select("Residues", "byres Atoms")

@@ Line 16: / Line 16: @@
 * display distance objects in pymol
 * restrict distances between hydrogen-bond forming atoms only
 The script also runs a number of controls to verify that inputs and outputs exists/are suitable.
@@ Line 21: / Line 22: @@
 == Usage ==
   distancesRH obj, ref, dist, [chain, [output S/P/N, [show Y/N, [Hbonds Y/N, [aname]]]]]
 == Required Arguments ==
 * '''obj''' = object name
 * '''ref''' = reference amino acid id
@@ Line 56: / Line 51: @@
 distancesRH 1LVM, 151, 3, B, P, Y, Y, N
 </source>
-Will show distances between CB of residue 151 in chain B of 1LVM and all atoms within 3 Å. Distances are limited to atoms that can form hydrogen bonds and will be printed in "dist_rH_151_N.txt". Dist objects will be shown in pymol.
+Will show distances between N of residue 151 in chain B of 1LVM and all atoms within 3 Å. Distances are limited to atoms that can form hydrogen bonds and will be printed in "dist_rH_151_N.txt". Dist objects will be shown in pymol.

← Older revision		Revision as of 16:32, 2 January 2013
Line 25:		Line 25:

	'''Note #1:''' the selected molecule must be visible.		'''Note #1:''' the selected molecule must be visible.
−	'''Note #2:''' soon a version that ~~manages~~ multiple states.	+
		+	'''Note #2:''' soon a version that handles multiple states.