1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
|
Installation and Usage Notes for the Validation Application
(Source Distribution)
Note: It is highly recommended to utilize binary distribution,
since it contains an additional submodule, called PROCHECK, which does more
structure checking. This source distribution does not contain PROCHECK.
1. Installation
a. Uncompress and unbundle the distribution using the following command:
zcat validation-vX.XXX-XXX.tar.gz | tar -xf -
The result of this command is a subdirectory validation-vX.XXX-XXX in the
current directory. It contains subdirectories of various source modules
and the following items important for the user:
bin - subdirectory in which the application executable "validation-v8"
will be placed after the build process.
data - subdirectory that contains some data files needed by the
application.
b. Set up the environment variables.
- Define the RCSBROOT environment variable to point to the installation
directory. Note that the RCSBROOT environment is also used for other RCSB
applications like ADIT and PDB_EXTRACT. If all these applications are
running on a computer, the last instance of setenv command will define the
environment. Thus, set the environment at the command line as follows,
just prior to running the application. Assuming that the installation
directory is
/home/username/validation-vX.XXX-XXX, execute in the shell:
For C shell users:
setenv RCSBROOT /home/username/validation-vX.XXX-XXX
For Bourne shell users:
RCSBROOT=/home/username/validation-vX.XXX-XXX; export RCSBROOT
- Add "bin" subdirectory to the PATH environment variable.
Execute in the shell:
For C shell users:
setenv PATH "$RCSBROOT/bin:"$PATH
For Bourne shell users:
PATH="$RCSBROOT/bin:"$PATH; export PATH
2. Building the Application
a. Position in the validation-vX.XXX-XXX directory and run "make" command:
cd validation-vX.XXX-XXX
make
The application executable "validation-v8" will be placed in the "bin"
subdirectory.
NOTE: The users who are working on Sun platform are strongly advised to
check the compiler flags in etc/make.platform.sunos5 file. Depending on
the compiler version, users may be required to make modifications to those
compiler flags.
b. Make binary data from ASCII data
- Position in the validation-vX.XXX-XXX directory and run "make" command as
follows:
make binary
This command will create certain binary data files, using the ASCII data
files in data/ascii directory. The resulting files are stored in
data/binary directory. Note that it may take several minutes for this
step to complete. This step must be executed before the tool can be
utilized.
3. Application Usage Notes
Usage:
For mmCIF files (Please note, only mmCIF format files downloaded from the PDB
or generated by PDB_EXTRACT should be used):
validation-v8 -f file_name -o 2 -adit -exchange -public
For PDB files:
validation-v8 -f file_name -o 0 -adit
For example, to create reports for a file in mmCIF format named 1xyz.cif
type:
validation-v8 -f 1xyz.cif -o 2 -adit -exchange -public
Output:
The names of the output files begin with the root identifier <ID>,
which is followed by an extension that indicates the file type.
For a PDB format file, the program converts the file name without
extension into uppercase for the <ID>. For an mmCIF format file, the program
uses data block identifier as the <ID>.
The application creates the following files:
A. <ID>.letter: a text file that contains a summary validation letter.
B. <ID>.ps: a PostScript file that contains molecular graphics of the structure.
For crystal structures, this includes a view of the asymmetric unit
and crystal packing. If the mmCIF file was validated and the biological unit
of the entry is either larger or smaller than the asymmetric unit, and the
struct_biol_gen category was appropriately completed in the mmCIF
file, then a view of the biological unit(s) will be included.
For NMR ensemble structures, a view of the first model and the ensemble
of all models is included. If the NMR entry contains one model, a view
of the model will be included.
NUCHECK output: If the structure contains nucleic acids, the <ID>.ps file
also includes plots describing the geometry, torsion, and base morphology of
the nucleic acids generated by the program NUCHECK.
C. <ID>.html: This html file is an Atlas summary containing the following:
For all structures:
The sequence of the residues in each chain (from entity_poly for a mmCIF file,
from SEQRES for a PDB file, or from the coordinates if entity_poly or SEQRES
are not provided).
Citation information (if provided).
Refinement information (if provided).
For crystal structures, additional information is listed:
Space group and cell constants.
Crystallization conditions (if provided).
Refinement information (if provided).
3. REFERENCES
NUCHECK:
Zukang Feng, John Westbrook, Helen M. Berman. NUCheck: Rutgers University,
New Brunswick, NJ; 1998. Report No.: NDB-407.
|
GitWeb