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<div style="text-align: center">topmask: version 2.231.418d045(2020-03-01 18:49) [CATs - Conversion And Analysis Tools]</div>'''Name'''

<span style="margin-left: 15px;">topmask</span>

'''Synopsis'''

<span style="color: maroon; margin-left: 15px;">topmask</span> <span style="color: blue;">[OPTIONS]</span> [--] <span style="color: purple;">PARM</span> <span style="color: purple;">MASK</span>

'''Description'''

<p style="text-indent: 1em; text-align: justify;">Print the names of atoms or residues selected by the application of MASK. Current implementation fully supports ambmask syntax (see AMBER manual).</p>

'''Arguments'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
| <span style="color: purple;">PARM</span><br/><div style="margin-left: 30px;">topology file name. If - is provided then topology is read from standard input stream.</div>
|- style="vertical-align: top;"
| <span style="color: purple;">MASK</span><br/><div style="margin-left: 30px;">mask specification</div>
|}

'''Options'''

{| style="margin-left: 2em; width: 95%;"
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-c, --coords CRD</span><br/><div style="margin-left: 30px;">optional coordinates in AMBER coordinate format, coordinates are mandatory for masks containing distance operators (: @)</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-f, --maskfile</span><br/><div style="margin-left: 30px;">read mask specification from the first line of the file of name MASK. This option is suitable for the specification of very long masks.</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-r, --residues</span><br/><div style="margin-left: 30px;">perform selection on the level of residues. The mask specification cannot contains atom selectors (@ @ @%).</div>
|- style="vertical-align: top;"
|<span style="color: blue;">-o, --output FORMAT</span><br/><div style="margin-left: 30px;">specify output format. Default format 'cats' prints atoms or residues as the list sorted into three colums. Format 'list' prints the same information as 'cats' but only to a single colum without any header. Format 'number' prints only the number of selected atoms or residues. Format 'amber' provides the same output as ambmask. Format 'bmask' write bitmap mask.</div><span style="color:purple; margin-left: 30px;">(Default: cats)</span>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-v, --verbose</span><br/><div style="margin-left: 30px;">increase output verbosity</div>
|- style="vertical-align: top;"
|<span style="color: blue;">--version</span><br/><div style="margin-left: 30px;">output version information and exit</div>
|- style="vertical-align: top; background-color: #e6e6e6;"
|<span style="color: blue;">-h, --help</span><br/><div style="margin-left: 30px;">display this help and exit</div>
|}