1<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
2<tr bgcolor="#FFFFCC">
3<th align="left">Qualifier</th>
4<th align="left">Type</th>
5<th align="left">Description</th>
6<th align="left">Allowed values</th>
7<th align="left">Default</th>
8</tr>
9
10<tr bgcolor="#FFFFCC">
11<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
12</tr>
13
14<tr bgcolor="#FFFFCC">
15<td>[-infile]<br>(Parameter 1)</td>
16<td>infile</td>
17<td>Clean protein structure coordinates file</td>
18<td>Input file</td>
19<td><b>Required</b></td>
20</tr>
21
22<tr bgcolor="#FFFFCC">
23<td>-chainnumber</td>
24<td>integer</td>
25<td>Number of the chain for which torsion angles should be calculated</td>
26<td>Integer 1 or more</td>
27<td>1</td>
28</tr>
29
30<tr bgcolor="#FFFFCC">
31<td>-startresiduenumber</td>
32<td>integer</td>
33<td>First residue in chain for which torsion angles should be calculated</td>
34<td>Integer 1 or more</td>
35<td>1</td>
36</tr>
37
38<tr bgcolor="#FFFFCC">
39<td>-finishresiduenumber</td>
40<td>integer</td>
41<td>Last residue in chain for which torsion angles should be calculated (1 = last residue)</td>
42<td>Any integer value</td>
43<td>1</td>
44</tr>
45
46<tr bgcolor="#FFFFCC">
47<td>[-outfile]<br>(Parameter 2)</td>
48<td>report</td>
49<td>Output report file name</td>
50<td>(default -rformat table)</td>
51<td><i>&lt;*&gt;</i>.psiphi</td>
52</tr>
53
54<tr bgcolor="#FFFFCC">
55<th align="left" colspan=5>Additional (Optional) qualifiers</th>
56</tr>
57
58<tr>
59<td colspan=5>(none)</td>
60</tr>
61
62<tr bgcolor="#FFFFCC">
63<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
64</tr>
65
66<tr>
67<td colspan=5>(none)</td>
68</tr>
69
70<tr bgcolor="#FFFFCC">
71<th align="left" colspan=5>Associated qualifiers</th>
72</tr>
73
74<tr bgcolor="#FFFFCC">
75<td align="left" colspan=5>"-outfile" associated report qualifiers
76</td>
77</tr>
78
79<tr bgcolor="#FFFFCC">
80<td> -rformat2<br>-rformat_outfile</td>
81<td>string</td>
82<td>Report format</td>
83<td>Any string</td>
84<td>table</td>
85</tr>
86
87<tr bgcolor="#FFFFCC">
88<td> -rname2<br>-rname_outfile</td>
89<td>string</td>
90<td>Base file name</td>
91<td>Any string</td>
92<td>&nbsp;</td>
93</tr>
94
95<tr bgcolor="#FFFFCC">
96<td> -rextension2<br>-rextension_outfile</td>
97<td>string</td>
98<td>File name extension</td>
99<td>Any string</td>
100<td>&nbsp;</td>
101</tr>
102
103<tr bgcolor="#FFFFCC">
104<td> -rdirectory2<br>-rdirectory_outfile</td>
105<td>string</td>
106<td>Output directory</td>
107<td>Any string</td>
108<td>&nbsp;</td>
109</tr>
110
111<tr bgcolor="#FFFFCC">
112<td> -raccshow2<br>-raccshow_outfile</td>
113<td>boolean</td>
114<td>Show accession number in the report</td>
115<td>Boolean value Yes/No</td>
116<td>N</td>
117</tr>
118
119<tr bgcolor="#FFFFCC">
120<td> -rdesshow2<br>-rdesshow_outfile</td>
121<td>boolean</td>
122<td>Show description in the report</td>
123<td>Boolean value Yes/No</td>
124<td>N</td>
125</tr>
126
127<tr bgcolor="#FFFFCC">
128<td> -rscoreshow2<br>-rscoreshow_outfile</td>
129<td>boolean</td>
130<td>Show the score in the report</td>
131<td>Boolean value Yes/No</td>
132<td>Y</td>
133</tr>
134
135<tr bgcolor="#FFFFCC">
136<td> -rstrandshow2<br>-rstrandshow_outfile</td>
137<td>boolean</td>
138<td>Show the nucleotide strand in the report</td>
139<td>Boolean value Yes/No</td>
140<td>Y</td>
141</tr>
142
143<tr bgcolor="#FFFFCC">
144<td> -rusashow2<br>-rusashow_outfile</td>
145<td>boolean</td>
146<td>Show the full USA in the report</td>
147<td>Boolean value Yes/No</td>
148<td>N</td>
149</tr>
150
151<tr bgcolor="#FFFFCC">
152<td> -rmaxall2<br>-rmaxall_outfile</td>
153<td>integer</td>
154<td>Maximum total hits to report</td>
155<td>Any integer value</td>
156<td>0</td>
157</tr>
158
159<tr bgcolor="#FFFFCC">
160<td> -rmaxseq2<br>-rmaxseq_outfile</td>
161<td>integer</td>
162<td>Maximum hits to report for one sequence</td>
163<td>Any integer value</td>
164<td>0</td>
165</tr>
166
167<tr bgcolor="#FFFFCC">
168<th align="left" colspan=5>General qualifiers</th>
169</tr>
170
171<tr bgcolor="#FFFFCC">
172<td> -auto</td>
173<td>boolean</td>
174<td>Turn off prompts</td>
175<td>Boolean value Yes/No</td>
176<td>N</td>
177</tr>
178
179<tr bgcolor="#FFFFCC">
180<td> -stdout</td>
181<td>boolean</td>
182<td>Write first file to standard output</td>
183<td>Boolean value Yes/No</td>
184<td>N</td>
185</tr>
186
187<tr bgcolor="#FFFFCC">
188<td> -filter</td>
189<td>boolean</td>
190<td>Read first file from standard input, write first file to standard output</td>
191<td>Boolean value Yes/No</td>
192<td>N</td>
193</tr>
194
195<tr bgcolor="#FFFFCC">
196<td> -options</td>
197<td>boolean</td>
198<td>Prompt for standard and additional values</td>
199<td>Boolean value Yes/No</td>
200<td>N</td>
201</tr>
202
203<tr bgcolor="#FFFFCC">
204<td> -debug</td>
205<td>boolean</td>
206<td>Write debug output to program.dbg</td>
207<td>Boolean value Yes/No</td>
208<td>N</td>
209</tr>
210
211<tr bgcolor="#FFFFCC">
212<td> -verbose</td>
213<td>boolean</td>
214<td>Report some/full command line options</td>
215<td>Boolean value Yes/No</td>
216<td>Y</td>
217</tr>
218
219<tr bgcolor="#FFFFCC">
220<td> -help</td>
221<td>boolean</td>
222<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
223<td>Boolean value Yes/No</td>
224<td>N</td>
225</tr>
226
227<tr bgcolor="#FFFFCC">
228<td> -warning</td>
229<td>boolean</td>
230<td>Report warnings</td>
231<td>Boolean value Yes/No</td>
232<td>Y</td>
233</tr>
234
235<tr bgcolor="#FFFFCC">
236<td> -error</td>
237<td>boolean</td>
238<td>Report errors</td>
239<td>Boolean value Yes/No</td>
240<td>Y</td>
241</tr>
242
243<tr bgcolor="#FFFFCC">
244<td> -fatal</td>
245<td>boolean</td>
246<td>Report fatal errors</td>
247<td>Boolean value Yes/No</td>
248<td>Y</td>
249</tr>
250
251<tr bgcolor="#FFFFCC">
252<td> -die</td>
253<td>boolean</td>
254<td>Report dying program messages</td>
255<td>Boolean value Yes/No</td>
256<td>Y</td>
257</tr>
258
259<tr bgcolor="#FFFFCC">
260<td> -version</td>
261<td>boolean</td>
262<td>Report version number and exit</td>
263<td>Boolean value Yes/No</td>
264<td>N</td>
265</tr>
266
267</table>
268