|
|
Line 1: |
Line 1: |
− | __NOTOC__
| + | dummy |
− | yBGjWg <a href="http://uqruiyspbibn.com/">uqruiyspbibn</a>, [url=http://tggakcrzgvng.com/]tggakcrzgvng[/url], [link=http://neluvsnolxvj.com/]neluvsnolxvj[/link], http://efrsqjwzyioc.com/
| |
− | | |
− | == Description ==
| |
− | | |
− | This script is used for extracting structural properties for
| |
− | a set of structures in an ensemble. It requires a tag as argument to
| |
− | identify the structure set and either one of the options
| |
− | <B>-show</B> or <B>-prop</B>.<BR>
| |
− | The option <B>-prop</B> is used with a comma-separated list of
| |
− | property tags to extract the corresponding data written
| |
− | to standard output. The output consists of data columns
| |
− | in the same order as the tags are given in the list argument.
| |
− | The option <B>-show</B> is available to print the tags for
| |
− | all available properties.<BR>
| |
− | The following tags are commonly available:<BR><BR>
| |
− | <TABLE CELLPADDING=1 CELLSPACING=1>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>etot</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>total energy</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>eelec</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>electrostatic energy</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>evdw</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>van der Waals energy</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>egb</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>Generalized Born energy</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>esasa</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>Hydrophobic solvation energy</FONT></TD>
| |
− | </TR>
| |
− | <TR><TD></TD></TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rgyr</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>radius of gyration</FONT></TD>
| |
− | </TR>
| |
− | <TR><TD></TD></TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rmsdall</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>total RMSD from native</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rmsdca</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>C-alpha RMSD from native</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rmsdback</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>backbone RMSD from native</FONT></TD>
| |
− | </TR>
| |
− | <TR><TD></TD></TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rmsdpol</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>polar RMS distance from center</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rmsdhyd</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>hydrophobic RMS distance from center</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rmsdchg</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>charged RMS distance from center</FONT></TD>
| |
− | </TR>
| |
− | <TR><TD></TD></TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rmsdphi</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>phi dihed. RMSD from native</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rmsdpsi</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>psi dihed. RMSD from native</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rmsdchi1</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>chi1 dihed. RMSD from native</FONT></TD>
| |
− | </TR>
| |
− | <TR><TD></TD></TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>pphi</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>percent correct phi</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>ppsi</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>percent correct psi</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>pchi1</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>percent correct chi1</FONT></TD>
| |
− | </TR>
| |
− | <TR><TD></TD></TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>cont</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>fraction of native contacts</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>rho</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>fraction of native contacts</FONT></TD>
| |
− | </TR>
| |
− | <TR>
| |
− | <TD><FONT FACE=courier SIZE=3>gdtts</FONT></TD>
| |
− | <TD><FONT FACE=sans-serif,ARIAL,HELVETICA SIZE=3>GDT similarity from native</FONT></TD>
| |
− | </TR>
| |
− | </TABLE>
| |
− | <BR>
| |
− | This script only extracts data that has been previously
| |
− | calculated. In order to calculate structural properties for
| |
− | a whole ensemble see <docmark>calcprop.pl</docmark>. Properties
| |
− | may be set from external data with <docmark>setprop.pl</docmark>.
| |
− | <BR><BR>
| |
− | If the option <B>-score</B> is given a single score is calculated
| |
− | from the property values of all ensemble structures and written
| |
− | out instead of the whole list. The most common use would
| |
− | be to calculate simple averages with <B>-score avg</B>.
| |
− | Values that lie outside a given multiple
| |
− | of the standard deviation can be excluded as in
| |
− | <docmark>bestcluster.pl</docmark> by using <font color=#508060>avglow</font> or
| |
− | <font color=#508060>avgcent</font> as key words instead of <font color=#508060>avg</font>.
| |
− | The option <B>-limstd</B> is available to modify the value of
| |
− | the multiple used in this case.<BR><BR>
| |
− | The option <B>-cluster</B> is available to extract only data for
| |
− | structures in a certain cluster. Clusters can be calculated with
| |
− | <docmark>enscluster.pl</docmark>. If cluster information is only
| |
− | available for a different tag in the same ensemble the tag can
| |
− | be given with <B>-ctag</B> so that the corresponding cluster
| |
− | data is used instead. The <B>-cluster</B>
| |
− | option may be combined with <B>-score</B> to obtain a score for
| |
− | conformations in a given cluster.
| |
− | | |
− | == Options ==
| |
− | | |
− | ; -help : usage information
| |
− | | |
− | | |
− | == Examples ==
| |
− | | |
− | <mmtsbToolExample cmd="getprop.pl" set="/apps/mmtsb/bench/getprop.pl-test/test1"></mmtsbToolExample>
| |
− | | |
− | <mmtsbToolExample cmd="getprop.pl" set="/apps/mmtsb/bench/getprop.pl-test/test2"></mmtsbToolExample>
| |
− | | |
− | <mmtsbToolExample cmd="getprop.pl" set="/apps/mmtsb/bench/getprop.pl-test/test3"></mmtsbToolExample>
| |
− | | |
− | <mmtsbToolExample cmd="getprop.pl" set="/apps/mmtsb/bench/getprop.pl-test/test4"></mmtsbToolExample>
| |
− | | |
− | <mmtsbToolExample cmd="getprop.pl" set="/apps/mmtsb/bench/getprop.pl-test/test5"></mmtsbToolExample>
| |