My software notes

June 17, 2011

Ramachandran space of Glycine and Proline

Filed under: softwares and scripts — kpwu @ 6:26 pm
Tags: , ,

The following two plots are made according to the statistical values provided by the Richardson group. I download the KINEMAGE format of Glycine and Proline. Inside the two files, core and allowed regions are defined and can be extracted to make my own Ramachandran plot.

The defined core and allowed regions are also shown in this blog post.

Core and Allowed regions for Glycine in the Rama plot:

=== CORE REGIONS ====
== region 1====

-180 147.5
-172.5 147.5
-172.5 142.5
-162.5 142.5
-162.5 137.5
-157.5 137.5
-157.5 132.5
-137.5 132.5
-137.5 127.5
-107.5 127.5
-107.5 122.5
-82.5 122.5
-82.5 117.5
-77.5 117.5
-77.5 112.5
-52.5 112.5
-52.5 117.5
-47.5 117.5
-47.5 122.5
-42.5 122.5
-42.5 142.5
-47.5 142.5
-47.5 152.5
-52.5 152.5
-52.5 162.5
-57.5 162.5
-57.5 180
=== region 2=====
-117.5 37.5
-117.5 32.5
-122.5 32.5
-122.5 27.5
-127.5 27.5
-127.5 22.5
-132.5 22.5
-132.5 17.5
-137.5 17.5
-137.5 7.5
-132.5 7.5
-132.5 2.5
-127.5 2.5
-127.5 -7.5
-122.5 -7.5
-122.5 -17.5
-117.5 -17.5
-117.5 -22.5
-112.5 -22.5
-112.5 -27.5
-102.5 -27.5
-102.5 -32.5
-97.5 -32.5
-97.5 -37.5
-92.5 -37.5
-92.5 -42.5
-87.5 -42.5
-87.5 -47.5
-82.5 -47.5
-82.5 -52.5
-77.5 -52.5
-77.5 -57.5
-72.5 -57.5
-72.5 -62.5
-42.5 -62.5
-42.5 -57.5
-37.5 -57.5
-37.5 -42.5
-42.5 -42.5
-42.5 -27.5
-47.5 -27.5
-47.5 -17.5
-52.5 -17.5
-52.5 -7.5
-57.5 -7.5
-57.5 2.5
-62.5 2.5
-62.5 7.5
-67.5 7.5
-67.5 12.5
-72.5 12.5
-72.5 17.5
-77.5 17.5
-77.5 27.5
-82.5 27.5
-82.5 32.5
-87.5 32.5
-87.5 37.5
-117.5 37.5
==== region 3 =====
-180 -147.5
-162.5 -147.5
-162.5 -152.5
-152.5 -152.5
-152.5 -147.5
-147.5 -147.5
-147.5 -152.5
-132.5 -152.5
-132.5 -147.5
-127.5 -147.5
-127.5 -142.5
-122.5 -142.5
-122.5 -137.5
-117.5 -137.5
-117.5 -132.5
-112.5 -132.5
-112.5 -127.5
-107.5 -127.5
-107.5 -122.5
-92.5 -122.5
-92.5 -132.5
-87.5 -132.5
-87.5 -137.5
-82.5 -137.5
-82.5 -142.5
-77.5 -142.5
-77.5 -152.5
-72.5 -152.5
-72.5 -162.5
-67.5 -162.5
-67.5 -172.5
-62.5 -172.5
-62.5 -177.5
-57.5 -177.5
-57.5 -180
==== region 4 =====
62.5 180
62.5 172.5
67.5 172.5
67.5 162.5
72.5 162.5
72.5 152.5
77.5 152.5
77.5 142.5
82.5 142.5
82.5 137.5
87.5 137.5
87.5 132.5
92.5 132.5
92.5 122.5
107.5 122.5
107.5 127.5
112.5 127.5
112.5 132.5
117.5 132.5
117.5 137.5
122.5 137.5
122.5 142.5
127.5 142.5
127.5 147.5
132.5 147.5
132.5 152.5
147.5 152.5
147.5 147.5
152.5 147.5
152.5 152.5
162.5 152.5
162.5 147.5
180 147.5
=== region 5 ====
42.5 62.5
42.5 57.5
37.5 57.5
37.5 42.5
42.5 42.5
42.5 27.5
47.5 27.5
47.5 17.5
52.5 17.5
52.5 7.5
57.5 7.5
57.5 -2.5
62.5 -2.5
62.5 -7.5
67.5 -7.5
67.5 -12.5
72.5 -12.5
72.5 -17.5
77.5 -17.5
77.5 -27.5
82.5 -27.5
82.5 -32.5
87.5 -32.5
87.5 -37.5
117.5 -37.5
117.5 -32.5
122.5 -32.5
122.5 -27.5
127.5 -27.5
127.5 -22.5
132.5 -22.5
132.5 -17.5
137.5 -17.5
137.5 -7.5
132.5 -7.5
132.5 -2.5
127.5 -2.5
127.5 7.5
122.5 7.5
122.5 17.5
117.5 17.5
117.5 22.5
112.5 22.5
112.5 27.5
102.5 27.5
102.5 32.5
97.5 32.5
97.5 37.5
92.5 37.5
92.5 42.5
87.5 42.5
87.5 47.5
82.5 47.5
82.5 52.5
77.5 52.5
77.5 57.5
72.5 57.5
72.5 62.5
42.5 62.5
=== region 6====
57.5 -180
57.5 -162.5
52.5 -162.5
52.5 -152.5
47.5 -152.5
47.5 -142.5
42.5 -142.5
42.5 -122.5
47.5 -122.5
47.5 -117.5
52.5 -117.5
52.5 -112.5
77.5 -112.5
77.5 -117.5
82.5 -117.5
82.5 -122.5
107.5 -122.5
107.5 -127.5
137.5 -127.5
137.5 -132.5
157.5 -132.5
157.5 -137.5
162.5 -137.5
162.5 -142.5
172.5 -142.5
172.5 -147.5
180 -147.5
=== ALLOWED REGION ====
==line 1===
-180 112.5
-172.5 112.5
-172.5 117.5
-152.5 117.5
-152.5 112.5
-137.5 112.5
-137.5 107.5
-127.5 107.5
-127.5 102.5
-117.5 102.5
-117.5 97.5
-107.5 97.5
-107.5 92.5
-102.5 92.5
-102.5 87.5
-97.5 87.5
-97.5 72.5
-102.5 72.5
-102.5 62.5
-107.5 62.5
-107.5 57.5
-112.5 57.5
-112.5 52.5
-122.5 52.5
-122.5 47.5
-137.5 47.5
-137.5 52.5
-152.5 52.5
-152.5 42.5
-157.5 42.5
-157.5 7.5
-152.5 7.5
-152.5 -2.5
-147.5 -2.5
-147.5 -12.5
-142.5 -12.5
-142.5 -22.5
-137.5 -22.5
-137.5 -32.5
-132.5 -32.5
-132.5 -47.5
-127.5 -47.5
-127.5 -52.5
-122.5 -52.5
-122.5 -62.5
-117.5 -62.5
-117.5 -72.5
-122.5 -72.5
-122.5 -82.5
-127.5 -82.5
-127.5 -87.5
-132.5 -87.5
-132.5 -97.5
-137.5 -97.5
-137.5 -112.5
-142.5 -112.5
-142.5 -117.5
-147.5 -117.5
-147.5 -122.5
-152.5 -122.5
-152.5 -127.5
-162.5 -127.5
-162.5 -122.5
-167.5 -122.5
-167.5 -117.5
-172.5 -117.5
-172.5 -112.5
-180 -112.5
=== line 2===
-47.5 -180
-47.5 -167.5
-52.5 -167.5
-52.5 -162.5
-57.5 -162.5
-57.5 -152.5
-62.5 -152.5
-62.5 -142.5
-67.5 -142.5
-67.5 -132.5
-72.5 -132.5
-72.5 -127.5
-77.5 -127.5
-77.5 -77.5
-42.5 -77.5
-42.5 -72.5
-32.5 -72.5
-32.5 -67.5
-27.5 -67.5
-27.5 -32.5
-32.5 -32.5
-32.5 -17.5
-37.5 -17.5
-37.5 -7.5
-42.5 -7.5
-42.5 2.5
-47.5 2.5
-47.5 7.5
-52.5 7.5
-52.5 17.5
-57.5 17.5
-57.5 22.5
-62.5 22.5
-62.5 32.5
-67.5 32.5
-67.5 72.5
-72.5 72.5
-72.5 92.5
-67.5 92.5
-67.5 97.5
-52.5 97.5
-52.5 102.5
-42.5 102.5
-42.5 107.5
-37.5 107.5
-37.5 112.5
-32.5 112.5
-32.5 117.5
-27.5 117.5
-27.5 142.5
-32.5 142.5
-32.5 152.5
-37.5 152.5
-37.5 162.5
-42.5 162.5
-42.5 180
=== line 3===
47.5 180
47.5 167.5
52.5 167.5
52.5 162.5
57.5 162.5
57.5 147.5
62.5 147.5
62.5 142.5
67.5 142.5
67.5 132.5
72.5 132.5
72.5 127.5
77.5 127.5
77.5 77.5
42.5 77.5
42.5 72.5
32.5 72.5
32.5 67.5
27.5 67.5
27.5 32.5
32.5 32.5
32.5 17.5
37.5 17.5
37.5 7.5
42.5 7.5
42.5 -2.5
47.5 -2.5
47.5 -7.5
52.5 -7.5
52.5 -17.5
57.5 -17.5
57.5 -22.5
62.5 -22.5
62.5 -32.5
67.5 -32.5
67.5 -77.5
72.5 -77.5
72.5 -92.5
67.5 -92.5
67.5 -97.5
52.5 -97.5
52.5 -102.5
42.5 -102.5
42.5 -107.5
37.5 -107.5
37.5 -112.5
37.5 -112.5
32.5 -112.5
32.5 -117.5
27.5 -117.5
27.5 -142.5
32.5 -142.5
32.5 -152.5
37.5 -152.5
37.5 -162.5
42.5 -162.5
42.5 -177.5
47.5 -177.5
47.5 -180
==== line 4 =====
180 -112.5
172.5 -112.5
172.5 -117.5
152.5 -117.5
152.5 -112.5
137.5 -112.5
137.5 -107.5
127.5 -107.5
127.5 -102.5
117.5 -102.5
117.5 -97.5
107.5 -97.5
107.5 -92.5
102.5 -92.5
102.5 -87.5
97.5 -87.5
97.5 -67.5
102.5 -67.5
102.5 -62.5
107.5 -62.5
107.5 -57.5
112.5 -57.5
112.5 -52.5
122.5 -52.5
122.5 -47.5
137.5 -47.5
137.5 -52.5
152.5 -52.5
152.5 -42.5
157.5 -42.5
157.5 -7.5
152.5 -7.5
152.5 2.5
147.5 2.5
147.5 12.5
142.5 12.5
142.5 22.5
137.5 22.5
137.5 32.5
132.5 32.5
132.5 47.5
127.5 47.5
127.5 52.5
122.5 52.5
122.5 77.5
127.5 77.5
127.5 87.5
132.5 87.5
132.5 97.5
137.5 97.5
137.5 112.5
142.5 112.5
142.5 117.5
147.5 117.5
147.5 122.5
152.5 122.5
152.5 127.5
162.5 127.5
162.5 122.5
167.5 122.5
167.5 117.5
172.5 117.5
172.5 112.5
180 112.5

Example of core and allowed region in the proline Rama plot

Defined core and allowed regions/edges for Proline  :

== CORE region 1 ===

Phi	Psi
-92.5	180.0
-92.5	177.5
-97.5	177.5
-97.5	142.5
-92.5	142.5
-92.5	122.5
-87.5	122.5
-87.5	117.5
-82.5	117.5
-82.5	112.5
-72.5	112.5
-72.5	107.5
-67.5	107.5
-67.5	112.5
-42.5	112.5
-42.5	117.5
-37.5	117.5
-37.5	147.5
-42.5	147.5
-42.5	157.5
-47.5	157.5
-47.5	167.5
-52.5	167.5
-52.5	172.5
-57.5	172.5
-57.5	177.5
-62.5	177.5
-62.5	180.0

== CORE region 2 ===

-62.5	-180.0
-62.5	-177.5
-72.5	-177.5
-72.5	-172.5
-87.5	-172.5
-87.5	-177.5
-92.5	-177.5
-92.5	-180.0

== CORE region 3 ===

-72.5	82.5
-82.5	82.5
-82.5	77.5
-87.5	77.5
-87.5	72.5
-92.5	72.5
-92.5	62.5
-87.5	62.5
-87.5	52.5
-82.5	52.5
-82.5	47.5
-77.5	47.5
-77.5	52.5
-72.5	52.5
-72.5	57.5
-67.5	57.5
-67.5	67.5
-72.5	67.5
-72.5	82.5

== CORE region 4 ===

-92.5	27.5
-97.5	27.5
-97.5	7.5
-102.5	7.5
-102.5	-2.5
-97.5	-2.5
-97.5	-12.5
-92.5	-12.5
-92.5	-22.5
-87.5	-22.5
-87.5	-27.5
-82.5	-27.5
-82.5	-32.5
-77.5	-32.5
-77.5	-42.5
-72.5	-42.5
-72.5	-52.5
-67.5	-52.5
-67.5	-57.5
-57.5	-57.5
-57.5	-62.5
-42.5	-62.5
-42.5	-57.5
-37.5	-57.5
-37.5	-27.5
-42.5	-27.5
-42.5	-17.5
-47.5	-17.5
-47.5	-12.5
-52.5	-12.5
-52.5	-2.5
-62.5	-2.5
-62.5	2.5
-67.5	2.5
-67.5	7.5
-77.5	7.5
-77.5	12.5
-82.5	12.5
-82.5	17.5
-87.5	17.5
-87.5	22.5
-92.5	22.5
-92.5	27.5

== ALLOWED region 1 ===

-112.5	180.0
-112.5	177.5
-112.5	142.5
-107.5	142.5
-107.5	122.5
-102.5	122.5
-102.5	112.5
-97.5	112.5
-97.5	82.5
-102.5	82.5
-102.5	42.5
-107.5	42.5
-107.5	37.5
-112.5	37.5
-112.5	-12.5
-107.5	-12.5
-107.5	-22.5
-102.5	-22.5
-102.5	-32.5
-97.5	-32.5
-97.5	-37.5
-92.5	-37.5
-92.5	-42.5
-87.5	-42.5
-87.5	-52.5
-82.5	-52.5
-82.5	-57.5
-77.5	-57.5
-77.5	-62.5
-72.5	-62.5
-72.5	-67.5
-62.5	-67.5
-62.5	-72.5
-32.5	-72.5
-32.5	-67.5
-27.5	-67.5
-27.5	-62.5
-22.5	-62.5
-22.5	-32.5
-27.5	-32.5
-27.5	-17.5
-32.5	-17.5
-32.5	-7.5
-37.5	-7.5
-37.5	-2.5
-42.5	-2.5
-42.5	2.5
-47.5	2.5
-47.5	7.5
-52.5	7.5
-52.5	12.5
-57.5	12.5
-57.5	17.5
-62.5	17.5
-62.5	22.5
-67.5	22.5
-67.5	37.5
-62.5	37.5
-62.5	47.5
-57.5	47.5
-57.5	97.5
-47.5	97.5
-47.5	102.5
-37.5	102.5
-37.5	107.5
-32.5	107.5
-32.5	112.5
-27.5	112.5
-27.5	152.5
-32.5	152.5
-32.5	167.5
-37.5	167.5
-37.5	172.5
-42.5	172.5
-42.5	177.5
-42.5	180.0

== ALLOWED region 2 ===

-42.5	-180.0
-42.5	-177.5
-47.5	-177.5
-47.5	-172.5
-52.5	-172.5
-52.5	-167.5
-62.5	-167.5
-62.5	-162.5
-67.5	-162.5
-67.5	-157.5
-92.5	-157.5
-92.5	-162.5
-102.5	-162.5
-102.5	-167.5
-107.5	-167.5
-107.5	-177.5
-112.5	-177.5
-112.5	-180.0
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