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

June 7, 2011

[CSRosetta] one bug found for 3.1 on Mac

Filed under: softwares and scripts — kpwu @ 3:45 pm
Tags: , ,

When I use CSRosetta 3.1 on my iMac, I always meet an error that the runCSrescore3.com can’t work properly. The best_model is not selected, therefore the script doesn’t generate a 3-column name.rms.rescore.txt at the end.

I might find where the bug is although it’s quite confused to me.

1. The extract_pdb3.com used in runCSrescore3.com contains only one line to extract all PDBs simulated from Rosetta 3.1 but the total number of extracted PDBs are not matched to the real number of simulated PDB. For example, I have 500 structures in the “silent.out“, the extract_pdb3.com only extracts the first 499 PDBs to the directory “output”. The latest PDB in silent.out is never extracted.

2. The way to fix is quite weird to me but it works. I edited the “silent.out” file, remove the latest line and save as a new file. Then re-run runCSrescore3.com, everything works smoothly.

Here is the last 2 lines in silent.out, one of my CSRosetta project:

132 L -89.994 0.000 0.000 -18.305 11.572 -10.761 -170.644 70.854 0.000 0.000 S_j001_00000020 
rm temp.default.out.list

I deleted the line containing “rm temp.default.out.list” and ran “runCSrescores3.com”, everything works as it should be.

NOTE: I also tested CSRosetta 3.1 on a Linux cluster, it’s not necessary for me to do such edition and there is no such error message I met. Very weird to me. Hope this found bug can help Mac users to run CSRosetta 3.x well.

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