ShowLigandWaters - Revision history

Bell: 13 revisions

2014-03-28T03:53:32Z

13 revisions

2013-09-02T09:54:34Z

2013-09-02T09:52:04Z

2013-09-02T09:49:35Z

2013-09-02T09:42:21Z

2013-09-02T09:28:23Z

2013-09-02T09:17:23Z

2013-09-02T09:16:58Z

2013-09-02T09:14:39Z

2013-09-02T09:07:04Z

@@ Line 61: / Line 61: @@
 Water molecules are shown.
 Distance between water molecules and O or N atoms of ligand are shown.
 Usage

@@ Line 11: / Line 11: @@
 This script detects waters molecules within a specified distance from the ligand.<br>
 Detected water molecules are shown as spheres.<br>
-Distances between <b>water<\b> molecules and O or N atoms of ligand (potential H-bonds) are shown by dotted lines and is maked an output file containing a list of distance between waters and ligand atoms and the number of interactions.
+Distances between water molecules and O or N atoms of ligand (potential H-bonds) are shown by dotted lines.<br>

@@ Line 9: / Line 9: @@
 == Introduction ==
-This script detects waters molecules within a specified distance from the ligand.
+This script detects waters molecules within a specified distance from the ligand.<br>
-Detected water molecules are shown as spheres.
+Detected water molecules are shown as spheres.<br>
-Distances between water molecules and O or N atoms of ligand (potential H-bonds) are shown by dotted lines and is maked an output file containing a list of distance between waters and ligand atoms and the number of interactions
+Distances between <b>water<\b> molecules and O or N atoms of ligand (potential H-bonds) are shown by dotted lines and is maked an output file containing a list of distance between waters and ligand atoms and the number of interactions.
@@ Line 28: / Line 28: @@
 <source lang="python">
 PyMOL>waters FAD, 2.8
 Total number of water molecules at 2.8 A from ligand FAD: 3
 Number of water molecules that interact with ligand: 3
 Number of interactions between water molecules and ligand: 4
 output file: waters.txt
 HOH residue 2002 -- and -- ['FAD', '1363', 'O1P']  --->  2.611289 A
 HOH residue 2002 -- and -- ['FAD', '1363', 'O5B']  --->  3.592691 A
@@ Line 48: / Line 45: @@
 Number of water molecules that interact with ligand: 3
 Number of interactions between water molecules and ligand: 4
 [[File:Example 1 FAD 1C0L.png|450px|example #1]]

@@ Line 10: / Line 10: @@
 == Introduction ==
 This script detects waters molecules within a specified distance from the ligand.
-Water molecules are shown.
+Detected water molecules are shown as spheres.
-Distance between water molecules and O or N atoms of ligand are shown and is maked an output file containing a list of distance between waters and ligand atoms and the number of interactions
+Distances between water molecules and O or N atoms of ligand (potential H-bonds) are shown by dotted lines and is maked an output file containing a list of distance between waters and ligand atoms and the number of interactions

@@ Line 76: / Line 76: @@
 Output
 -A file is produced containing a list of distance between waters and ligand atoms and the number of interactions
--A graphic output share the water molecules interacting whith the ligand atoms by showing the distances between them
+-A graphic output show the water molecules interacting whith the ligand atoms by showing the distances between them
 """

← Older revision	Revision as of 03:53, 28 March 2014
(No difference)

@@ Line 37: / Line 37: @@
 </source>
-output file: waters.py
+output file: waters.txt
 <source lang="python">

@@ Line 25: / Line 25: @@
 == Examples ==
-'''example #1'''
+'''example #1 on PDB structure (1C0L)'''
 <source lang="python">
-PyMOL>pairwise_dist 1efa and chain D, 1efa and chain B, 3, output=S, show=Y
+PyMOL>waters FAD, 2.8
-efa/D/DC/13/OP1 to 1efa/B/TYR/47/OH: 2.765
+Number of interactions between water molecules and ligand: 4
 </source>
-[[File:pairwise1.png|450px|example #1]]
+output file: waters.py

@@ Line 6: / Line 6: @@
 }}
-This is a test page########
 == Introduction ==