CHOPS RELEASE NOTES
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Convex Hull Of Protein Surface(CHOPS) program
by Wei Zheng (jlspzw139@sina.com)
(In this program, the comprehensive asa program--accall is generated by Naccess.
Hubbard, S.J. and Thornton, J.M. (1993) 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London.)
This program will calculate all k-th convex hulls of protein surface when input a protein pdb file (pdb format),
it is supplied in source code form along with the required data files and run under the windows/linux.
Support OS
Windows 7/8/8.1/10 Linux
If your system is windows and the version is earlier than vista(XP), update .NET to 4.0 or lastest released version from Microsoft.
Input file
protein_structure_file in pdb format.
How to use it?
Firstly we can download the CHOPS.tar in http://sourceforge.net/projects/chops/.
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Windows
Step one install gfortran:
Unzip this files,the gfortran-windows-20140629.exe needs to be installed in the first step if your OS is windows.
Check that you have indeed files in the directory you selected for installation (if you chose c:\gfortran as installation directory,
you should have directories like C:\Program Files\bin C:\Program Files\include ... you should also have a file gfortran.exe in C:\Program Files\bin .
Now we have to tell Windows to look in C:\Program Files\bin for the compiler. Right click on My Computer, Properties, Advanced Tab, Environment Variables.
In the top section labeled "User variables for..." there may or may not be an entry called PATH.
If there is, click on it, click edit, then add the following at the end of the line.
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;C:\Program Files\gfortran\bin;
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If there is not, click add.
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Variable Name: PATH
Variable Value: C:\Program Files\gfortran\bin;
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Click okay enough times to get back to the desktop, and open a new command prompt.
You can do this by either going to Start, Accessories, Command Prompt, or by clicking run, and typing in cmd.
If you have any problems, you can find help from gfortran website https://gcc.gnu.org/wiki/GFortranBinariesWindows .
Step two set ps script excutionpolicy:
In windows system(7/8/8.1/10),open my computer->all programs->Accessories->Windows Powershell->Windows Powershell.
In the Windows Powershell, we must run the relevant commands as adminstrator.
Then input the 'Set-ExecutionPolicy RemoteSigned' to get the execuate permissions of the Powershell script.Notice! You must run powershell as adminstrator(right click!).
Command:
If you want get some help,then type
./CHOPS.ps1 -help help
Notice!There are two word help.
In current directory, if we calculate one protein, we can run CHOPS.ps1 as:
./CHOPS.ps1 -infile input_pdb_file_path[Rooted] -outdir output_directory[Rooted] -mode all[default],single,interaction
-mode opition:
all: treat all chains in protein as a whole points set then calculate all k-th convex hull of protein surface.
single: calculate each chain in one protein as independent points set then calculate itself.
interaction: same as single mode, but define surface residue which is in 4 angstrom far from other chain's surface residue as convex hull 0.
Usage:
./CHOPS.ps1 -infile D:\CHOPS\example\1A2YC.pdb -outdir D:\CHOPS\exampleout -mode all
If we calculate the multiple proteins, first put all proteins in a directory, then we can run MutiCHOPS.ps1 as:
./MultiCHOPS.ps1 -indir input_pdbs_directory[Rooted] -outdir output_directory[Rooted] -mode all[default],single,interaction
Usage:
./MultiCHOPS.ps1 -indir D:\CHOPS\example\ -outdir D:\CHOPS\exampleout -mode single
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Linux
We give two version 32bit and 64bit binaries, you can choose one suit your OS.
If you want to use it, Mono.NET must be install in your linux first.
Step one Mono.Net
You can download MonoDevelop and get help from website http://monodevelop.com/ or Mono package.
The Chops package contains a compiled version mono-4.2.1 in linux/mono-4.2.1/ directory, and the mono-4.2.1 source code mono-4.2.1.102.tar.bz2 in linux/ directory.
You can run with default mono-4.2.1 packaged in Chops and change the variable $chopsdir to your own installl parth, If it doesn't work in your OS, please complie
mono-4.2.1 source code following the readme file in mono-4.2.1 source code. If you complie your own mono-4.2.1 change the variable $chopsdir $mono in CHOPS.sh,
MultiCHOPS.sh to your own install directory.
Step two Change variable
Change $chopsdir variable in CHOPS.sh and MultiCHOPS.sh, and if necessary change the mono exec install path $mono to your own path.
Command
In current directory, if we calculate one protein, we can run CHOPS.sh as:
./CHOPS.sh input_pdb_file_path output_directory mode=all[default],single,interaction
Usage:
./CHOPS.sh /home/usr/CHOPS/example/1A2YC.pdb /home/usr/CHOPS/exampleout all
If we calculate the multiple proteins, first put all proteins in a directory, then we can run MutiCHOPS.sh as:
./MultiCHOPS.sh input_pdbs_directory output_directory mode=all[default],single,interaction
Usage:
./MultiCHOPS.sh ../../example ../../exampleout single
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Result
result file will be written to a new pdb file with name ProteinName.sch.pdb. The k-th convex hull of protein surface information will be written to
beta-factor position,1.00,2.00,...represent the k-th surface convex hull, -1.00 represents the residues burried in protein, 0.00 represents surface
interaction residue.
sample result
ATOM 1 N MET C 1 94.766 87.569 60.599 1.00 0.00 N
ATOM 2 CA MET C 1 95.063 86.713 59.420 1.00 0.00 C
ATOM 3 C MET C 1 96.298 85.843 59.619 1.00 0.00 C
ATOM 4 O MET C 1 97.405 86.233 59.238 1.00 0.00 O
ATOM 5 CB MET C 1 95.282 87.593 58.195 1.00 0.00 C
ATOM 6 CG MET C 1 94.060 87.760 57.324 1.00 0.00 C
ATOM 7 SD MET C 1 94.423 87.384 55.596 1.00 0.00 S
ATOM 8 CE MET C 1 93.994 88.910 54.739 1.00 0.00 C
ATOM 9 N ASP C 2 96.119 84.674 60.225 1.00 0.00 N
ATOM 10 CA ASP C 2 97.237 83.757 60.428 1.00 0.00 C
ATOM 11 C ASP C 2 97.107 82.778 59.293 1.00 0.00 C
ATOM 12 O ASP C 2 96.112 82.065 59.183 1.00 0.00 O
ATOM 13 CB ASP C 2 97.113 83.050 61.773 1.00 0.00 C
ATOM 14 CG ASP C 2 96.495 83.945 62.843 1.00 0.00 C
ATOM 15 OD1 ASP C 2 97.115 84.999 63.165 1.00 0.00 O
ATOM 16 OD2 ASP C 2 95.393 83.611 63.360 1.00 0.00 O
ATOM 17 N ILE C 3 98.121 82.741 58.445 1.00 0.00 N
ATOM 18 CA ILE C 3 98.065 81.881 57.288 1.00 0.00 C
ATOM 19 C ILE C 3 99.213 80.888 57.244 1.00 0.00 C
ATOM 20 O ILE C 3 100.387 81.266 57.233 1.00 0.00 O
ATOM 21 CB ILE C 3 98.057 82.780 56.066 1.00 0.00 C
ATOM 22 CG1 ILE C 3 96.627 83.100 55.689 1.00 0.00 C
ATOM 23 CG2 ILE C 3 98.807 82.157 54.938 1.00 0.00 C
ATOM 24 CD1 ILE C 3 96.534 84.295 54.795 1.00 0.00 C
ATOM 1814 N LEU C 8 44.099 -13.128 15.182 0.00 8.00 N
ATOM 1815 CA LEU C 8 45.366 -13.153 14.437 0.00 8.00 C
ATOM 1816 C LEU C 8 45.486 -11.926 13.511 0.00 8.00 C
ATOM 1817 O LEU C 8 46.560 -11.328 13.402 0.00 8.00 O
ATOM 1818 CB LEU C 8 45.505 -14.452 13.632 0.00 8.00 C
ATOM 1819 CG LEU C 8 46.794 -14.674 12.831 0.00 8.00 C
ATOM 1820 CD1 LEU C 8 48.028 -14.660 13.745 0.00 8.00 C
ATOM 1821 CD2 LEU C 8 46.719 -16.000 12.109 0.00 8.00 C
ATOM 1822 N ALA C 9 44.382 -11.550 12.862 0.00 -1.00 N
ATOM 1823 CA ALA C 9 44.352 -10.385 11.969 0.00 -1.00 C
ATOM 1824 C ALA C 9 44.790 -9.110 12.714 0.00 -1.00 C
ATOM 1825 O ALA C 9 45.613 -8.338 12.218 0.00 -1.00 O
ATOM 1826 CB ALA C 9 42.934 -10.205 11.390 0.00 -1.00 C
ATOM 1827 N ALA C 10 44.236 -8.915 13.914 0.00 4.00 N
ATOM 1828 CA ALA C 10 44.560 -7.758 14.750 0.00 4.00 C
ATOM 1829 C ALA C 10 46.057 -7.732 15.115 0.00 4.00 C
ATOM 1830 O ALA C 10 46.707 -6.688 15.037 0.00 4.00 O
ATOM 1831 CB ALA C 10 43.688 -7.757 16.031 0.00 4.00 C
ATOM 1832 N ALA C 11 46.602 -8.881 15.504 0.00 6.00 N
ATOM 1833 CA ALA C 11 48.020 -8.966 15.858 0.00 6.00 C
ATOM 1834 C ALA C 11 48.912 -8.664 14.635 0.00 6.00 C
ATOM 1835 O ALA C 11 49.865 -7.884 14.714 0.00 6.00 O
ATOM 1836 CB ALA C 11 48.333 -10.349 16.435 0.00 6.00 C
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Please see the LICENSE file for the license terms of the software. It is
basically free for academic users, but a license fee applies to commercial
users.
THE PUBLICATION OF RESEARCH USING Our method MUST INCLUDE AN APPROPRIATE
CITATION TO THE METHOD:
Analysis of conformational B-cell epitopes in antibody-antigen complex using depth function and convex hull
Wei Zheng, Jishou Ruan, Gang Hu, Kui Wang and Jianzhao Gao
SHORT SUMMARY OF THE METHOD
In mathematics, the convex hull of a set X of points in the Euclidean space is the smallest convex set that contains X.
For instance, when X is a bounded subset of the plane, the convex hull may be visualized as the shape formed by a rubber
band stretched around X. For a protein, we consider all residues in a protein as a point set X.
For a protein, all convex hull residues of the protein is defined as the first level of convex hull. We denoted by CH1(X).
Remain residues of the protein are X-CH1(X). Then we can compute the convex hull of X-CH1(X), the convex hull of X-CH1(X) is
defined as CH2(X) and so on. we choose k-th convex hull residues on protein surface as k-th convex hull of protein surface.
change in beta version 2.0
1.Package complied mono-4.2.1 (64bit version ) and mono-4.2.1 source code in the chops linux package.
2.Change CHOPS.sh fit for multipy threading for linux version chops (generate random number temp file, and input parameter file for accall).
3.Change the CHOPS.sh script, it can run from any path.
