[Modeller] point mutation script

Saw a script provided by Modeller that can quickly mutate a point to any other residues.

Here is the linke <Mutate model python script by Modeller>

To use the script, just type command like the following line:
Example: python mutate_model.py 1t29 1699 LEU A > 1t29.log

Where mutate_model.py is the script provided by Modeller
1t29 is the PDB file name
1699 is the position for mutation
LEU is the new residue
A stands for chain number.

I have test this script at Modeller 9v11, it works very well and quickly.

[PyMOL] contact map (CMView)

In PyMOL Wiki, there is a “contact map visualizer” plugin providing users to inspect the protein intramolecular contacts. However, this plugin requires “PyGame”, “Tkinter”, “PIL (python image library)” and most importantly, Gromacs!

I used Fink (Mac OSX 10.6.8) to successfully install Gromacs 4.1 but Fink reported problems while installing pygame. So I can generate xpm file of target protein structure by Gromacs but not inspect the contact map in PyMOL.

In contrast, I found another contact map visualizer called “CMView – Protein contact map visualization and analysis“. This program is written in Java and uses PyMOL as the molecular viewer.

Installation note (work platform: Mac OSX 10.6.8 with X11)

1. Download the CMView file, unzip it and move the folder to proper path)

2.Edit the “cmview.cfg” file and correct the path of pymol execute. Optional programs such as DSSP and DALI can be used if installed.

3. In terminal, call “cmview.sh” and load the PDB file from “CMView” and enjoy visualizing the molecules.

While the PDB is loaded, the CMView (run in Java) will show you the contact map.  You can use mouse to crop the region of interest and instantly see the contacts in the PDB file.

change display font/size in Sparky

The default font size of Sparky in my 13″ macbook is way big thus I have to move spectrum windows around or move some spectra windows to other desktop. Here is a solution to reduce the font size and the default display sizes of “pointer mode”, “Sparky main window” and individual windows will be smaller (because font is smaller..).

Example of Sparky MacOSX version (should be similar to Linux version):

1. found the path of installed Sparky. My sparky was extracted and moved to “/Applications”.

2. Go the Sparky-home/Contents/Resources/lib (the path in Linux version may be different, however, I don’t have linux machine with me, can’t provide example path of it)

3. edit the file “Sparky” (using vi or nedit, for example),  find a section about “Fonts” and change the fonts/size. Personally I like font size = 10.

=== The example of the Fonts section in this lib/Sparky  file”=====

!
! Fonts
!
! normalFont: for labels, buttons, menus, axis scales, res panels …
! fixedWidthFont: for lists where columns should line up
! scalableFont: for contour plot assignment labels
!
Sparky.normalFont: -family lucida -size 10
Sparky.fixedWidthFont: -family courier -size 10
Sparky.scalableFont: -family courier

================================================

The two figures shown below are displayed with font sizes 10 (top) and 16 (bottom). Smaller font size in Sparky clearly uses less space in the whole desktop. (the two windows are equally scaled–see same size of window title “Sparky 3.115”)

install procheck on MacOS 10.6

Running system: MacOS X 10.6.8

First, followed by instruction of Procheck official site, download all required file. (you need to fax the license agreement first).

I use tar command to uncompress the procheck.tar.gz and aqua3.2.tar.gz.

Secondly, in procheck folder, edit the Makefile and change two lines:

F77 = gfortran # Your FORTRAN compiler
CC = gcc # Your C compiler

I have two F77 compilers, g77 and gfortran in my Mac 10.6.8 X11 environment. g77 was failed to compile the fortran macros but gfortran does very well. The gfortran package can be installed through fink. (similar solution/discussion at CCP4bb forum)

Step 3: After modifying the “Makefile”, simply type “make” at procheck folder and you will see several warnings but the required executable  macros will be generated (e.g. vplot…).

Step 4: copy the cshrc section preloaded in setup.sh to your .cshrc (or .tcsrch) file, remember to update the absolute path of your procheck (e.g. /User/admin/program/procheck). You have to update the path at “set    prodir” and “setenv   prodir“— two lines.

After updating the C shell environment (source $HOME/.cshrc), I successfully run Procheck analysis at my local iMac! Here are the example figures generated in my test run.

LigPlot on Mac OS X 10.6

A quick note of test of LigPlot on my Mac.

==background ===

If you have ever used the PDBSum service, you may notice many provided useful information including the protein-protein interaction/interface, protein-ligand or protein-DNA (or RNA) interaction/interface, Rama plot, topology and sequence.

For example (see image below), the banner of PDB file (2XUV) entry in PDBSum provides links of “protein, “ligands”, protein-protein interaction” and “clefts” for users to see the detail molecular interactions. When you click the link “ligands” in the banner or the “SO4” link in the “Contents” at left corner, you will see a image generated by LigPlot which shows both hydrophobic and hydrogen bonding interactions between ligand and protein.

=== installation on Mac =====

Following by the instruction described at LigPlot official site, I downloaded the LigPlot binary files (Linux/Unix version) to run it on my iMac (10.6.8).

After uncompressing the hbplus and ligplot file,  as instructed in the “install.doc” text file, 3 steps are essential to make ligplot run well on Mac OS 10.6:

1. user has to manually compile some files in ligplot (GCC must be installed first) :
cc -o ligplot ligplot.c -lm
cc -o hbadd hbadd.c -lm
cc -o dimer dimer.c

2. run “make” in the hbplus to compile all required C files.

3. edit either tcsh, csh or bash shell environment file as suggested in the “install.doc” file.

=== run LigPlot on Mac, an example ===

I have used HADDOCK to generate some protein-RNA docked model and LigPlot was used to see the protein-RNA contacts. Here is the example result:

 

Note: The ligplot author has another specific version called NucPlot to draw the protein-DNA or protein-RNA contacts, I didn’t try it because it just draw the molecular contacts in different style.

add protons (hydrogens) to structure

A list of online servers or programs as I know which can add hydrogens on the structures (most likely determined by X-ray crystallography).

1. WHATIF server (http://swift.cmbi.ru.nl/servers/html/index.html)
   –> check “Hydrogen (bonds)” in the left frame
2. Molprobity server (http://molprobity.biochem.duke.edu/)
   –> after uploading a PDB file, you will see “add hydrogen” in the online interface.
3. HAAD: (a computer algorithm for constructing hydrogen atoms from protein heavy-atom structures)
4. PyMOL (Win/Linux/Mac)
5. SPDB (Swiss PDB Viewer)

In my own test, WHATIF is more friendly for other CNS/Xplor-NIH/Haddock-related works because WHATIF generates CNS/Xplor compatible PDB format.

Molprobity generates PDB with added hydrogens but the added hydrogens are ALL numbered as “0”. Thus I have to use other program to reset all atom numbers.

PyMOL adds hydrogens,too (object -> A -> hydrogens -> add) but the nomenclature of hydrogens in proteins seems weird (see below). The hydrogens are named as H01, H02, H03.. etc. I don’t think CNS/Xplor-NIH can take it for further calculation purposes.

GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data

There is an article published at Journal of Biomolecular NMR recently which describes a package of MATLAB scripts to analyze CPMG relaxation dispersion NMR data. I haven’t done CPMG RD experiments on my target proteins, however, I know the analysis of CPMG RD data is not trivial. This program, GUARDD, seems to be a very useful and UI-friendly toolkit to efficiently obtain information of Rex, Kex and other relaxation rates from CPMG RD data.

The following snapshots are directly linked to GUARDD homepage.

More information about GUARDD:

Title: : GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data.
Journal: Journal of Biomolecular NMR (online published first, Dec.20. 2011)
Homepage at google code: http://code.google.com/p/guardd/ 

Additional information:
Matlab, a product from Mathworks
CATIA (Cpmg, Anti-trosy, and Trosy Intelligent Analysis) from Lewis Kay’s group
CPMGFit from Arther Palmer’s group

Bruker’s Topspin running on Mac

Balance the report as I just made a post for Agilent’s VnmrJ. 🙂

I found from a web blog article that introduces the news–Bruker’s Topspin 3.1 for Mac.

Bruker’s brief introduction of Topspin for Mac machine includes features:
(note on 10/29/2012, the introduction seems gone at Bruker’s website)

• Mac OS X platform for TopSpin processing
• Inspire a new generation of NMR users, experts and students alike
• Entirely programmed in the native Apple Mac OS X environmentData analysis, processing and simulation features for efficient small molecule and structural biology research
• Ideal data processing and analysis aid for NMR training

Snapshots of Topspin running on Mac linked to Bruker’s example images show at here:

(note on 10/29/2012 the image was removed from the blog)

According to Bruker’s purchase link, the price is $99 of academic license for one Mac machine. The computer MAC address code must be provided meaning one license is only available for one Mac machine!!

The current version (Oct of 2011) Topspin for Mac required “Core 2 Duo” type CPU and OS 10.6 (snow leopard and later). My old macbook pro with “core duo” is not available this time. Sad. I can only try to install it on my iMac.

Maybe I should email Bruker to request something like 30-60 days free trial and make some blog articles for “Bruker Topspin on Mac” as an exchange.

[software] MaxCluster

I was searching online for some scripts/macros that I can use them to superimpose and compare the RMSD of two proteins (same sequence) based on my calculated results. I know PyMOL and MOLMOL provide such tools however I have tons of protein candidates to be compared.

Before I start to write the script by myself, I checked online and saw this software “MaxCluster” developed by the “Structural Bioinformatics group in Imperial College London” . This program can do all atom or backbone RMSD calculation (superposition/alignment too) as well as ensemble clustering. It works pretty FAST!! I used many times recently. To compare more than 3000 structures, it returns me the results in one minutes.

Good for try.

 

Ramachandran space of Glycine and Proline

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