Summary

• Page properties (1 modified, 0 added, 0 removed)
• Attachments (0 modified, 1 added, 0 removed)
  • CodeCogsEqn-58.png

Details

Page properties

Content

...	...	@@ -12,15 +12,36 @@
12	12	(((
13	13	(% class="col-xs-12 col-sm-8" %)
14	14	(((
15		-= What can I find here? =
	15	+= What DF matrices are? =
16	16
17		-* Notice how the table of contents on the right
18		-* is automatically updated
19		-* to hold this page's headers
	17	+The analysis of the results of a MD simulation can performed using the Distance Fluctuation matrices (DF), based on the Coordination Propensity hypothesis:
20	20
21		-= Who has access? =
	19	+(% style="text-align:center" %)
	20	+[[image:CodeCogsEqn-58.png||height="34" width="181"]]
22	22
23		-Describe the audience of this collab.
	22	+low CP values, corresponding to low pair-distance fluctuations, highlight groups of residues that move in a mechanically coordinated way.
	23	+
	24	+
	25	+= How to use the script =
	26	+
	27	+• __Requisites__
	28	+
	29	+ - Python 3.0 (or newer version)
	30	+
	31	+ - Numpy
	32	+
	33	+ - Scipy
	34	+
	35	+
	36	+• __Usage__
	37	+
	38	+The script can analyze a MD trajectory and identify the coordinated motions between residues. It can then filter the output matrix based on the distance to identify long-range coordinated motions.
	39	+
	40	+The script can work both using only C-alphas (using either a pdb or a xyz file) or the sidechains (using a pdb file).
	41	+
	42	+For more information run:
	43	+
	44	+{{{ python3 distance_fluctuation.py -h}}}
24	24	)))
25	25
26	26
...	...	@@ -28,8 +28,12 @@
28	28	(((
29	29	{{box title="**Contents**"}}
30	30	{{toc/}}
	52	+
	53	+
31	31	{{/box}}
32	32
33	33
34	34	)))
35	35	)))
	59	+
	60	+

CodeCogsEqn-58.png

Author

...	...	@@ -1,0 +1,1 @@
	1	+XWiki.emacasali

Size

...	...	@@ -1,0 +1,1 @@
	1	+7.0 KB

Content