<html> <head> <title> Garlic Commands </title> </head> <h1 align=center> Garlic Commands </h1> <hr size="3"> <font size="-1" color=RED> garlic, free molecular viewer and editor, free molecular visualization program, protein structure, DNA structure, PDB, molecular rendering, biological macromolecule, Unix, Linux, free software download, open source software, Damir Zucic. </font> <hr size="3"> The image in the main window is controled by <a href="../controls/index.html"> CONTROLS </a> and by COMMANDS. This page contains the list of garlic commands. <br><br> Garlic commands are strings, consisting of one or more words. A command is executed when you press the RETURN key (this key is labeled ENTER on some keyboards). Note that ENTER key on the numeric keypad (the one in the bottom right corner of your keyboard) is NOT the right key! Commands will be displayed in the area called the input window. <br><br> The input window is placed at the bottom of the main garlic window, left justified. You don't have to the click into this area to enter the command string - just type it. The input window is capable to display a single error message (top) and a single command (bottom). <br><br> You can access previously executed commands by using arrow keys on your keyboard (the UP arrow scans the history buffer backwards and DOWN arrow in the opposite direction). <br><br> This page contains the alphabetic list of garlic commands with a short description and with link to detailed description. <br><br> Commands are generally case insensitive, but file names are case sensitive because unix (linux) is case sensitive. <br><br> <hr size="3"> <table border=2 cellspacing=2 cellpading=0> <td align="left"> SHORT <br> FORM </td> <td align="left"> LONG FORM </td> <td align="left"> SHORT DESCRIPTION </td> <tr> <td align="left"> <a href="add.html"> ADD </a> </td> <td align="left"> ADD </td> <td align="left"> Expand current selection. </td> <tr> <td align="left"> <a href="ang.html"> ANG </a> </td> <td align="left"> ANGLE </td> <td align="left"> Define angle. </td> <tr> <td align="left"> <a href="ato.html"> ATO </a> </td> <td align="left"> ATOMS </td> <td align="left"> Change atom drawing style. </td> <tr> <td align="left"> <a href="bac.html"> BAC </a> </td> <td align="left"> BACKBONE </td> <td align="left"> Draw backbone. </td> <tr> <td align="left"> <a href="bg.html"> BACKG </a> </td> <td align="left"> BACKGROUND </td> <td align="left"> The same as BG. </td> <tr> <td align="left"> <a href="bal.html"> BAL </a> </td> <td align="left"> BALLS </td> <td align="left"> Set the ball radius. </td> <tr> <td align="left"> <a href="bg.html"> BG </a> </td> <td align="left"> BACKGROUND </td> <td align="left"> Change main window background color. </td> <tr> <td align="left"> <a href="blu.html"> BLU </a> </td> <td align="left"> BLUR </td> <td align="left"> Blur (soften) the image in the main window. </td> <tr> <td align="left"> <a href="bon.html"> BON </a> </td> <td align="left"> BONDS </td> <td align="left"> Change bond drawing style or refresh bonds. </td> <tr> <td align="left"> <a href="cat.html"> CAT </a> </td> <td align="left"> CATCH </td> <td align="left"> Catch the specified structure. </td> <tr> <td align="left"> <a href="cen.html"> CEN </a> </td> <td align="left"> CENTER </td> <td align="left"> Change the internal coordinate system origin. </td> <tr> <td align="left"> <a href="col.html"> COL </a> </td> <td align="left"> COLOR </td> <td align="left"> Set color. </td> <tr> <td align="left"> <a href="com.html"> COM </a> </td> <td align="left"> COMPARE </td> <td align="left"> Compare two sequences. </td> <tr> <td align="left"> <a href="cre.html"> CRE </a> </td> <td align="left"> CREATE </td> <td align="left"> Create structure. </td> <tr> <td align="left"> <a href="dis.html"> DIS </a> </td> <td align="left"> DISCARD </td> <td align="left"> Discard structure. </td> <tr> <td align="left"> <a href="doc.html"> DOC </a> </td> <td align="left"> DOCK </td> <td align="left"> Prepare two structures for docking. </td> <tr> <td align="left"> <a href="dum.html"> DUM </a> </td> <td align="left"> DUMP </td> <td align="left"> Dump some numeric data to console or to file. </td> <tr> <td align="left"> <a href="edi.html"> EDI </a> </td> <td align="left"> EDIT </td> <td align="left"> Edit structure. </td> <tr> <td align="left"> <a href="exe.html"> EXE </a> </td> <td align="left"> EXECUTE </td> <td align="left"> Execute garlic script. </td> <tr> <td align="left"> <a href="exi.html"> EXI </a> </td> <td align="left"> EXIT </td> <td align="left"> Quit garlic session. </td> <tr> <td align="left"> <a href="add.html"> EXP </a> </td> <td align="left"> EXPAND </td> <td align="left"> The same as ADD. </td> <tr> <td align="left"> <a href="fad.html"> FAD </a> </td> <td align="left"> FADING </td> <td align="left"> Change color fading style or parameter(s). </td> <tr> <td align="left"> <a href="fg.html"> FG </a> </td> <td align="left"> FOREGROUND </td> <td align="left"> Change main window foreground color. </td> <tr> <td align="left"> <a href="fon.html"> FON </a> </td> <td align="left"> FONT </td> <td align="left"> Change font. </td> <tr> <td align="left"> <a href="fg.html"> FOREG </a> </td> <td align="left"> FOREGROUND </td> <td align="left"> The same as FG. </td> <tr> <td align="left"> <a href="gro.html"> GRO </a> </td> <td align="left"> GROUP </td> <td align="left"> Group (catch simultaneously) the specified structures. </td> <tr> <td align="left"> <a href="hid.html"> HID </a> </td> <td align="left"> HIDE </td> <td align="left"> Hide selected atoms. </td> <tr> <td align="left"> <a href="hyb.html"> HYB </a> </td> <td align="left"> HYBONDS </td> <td align="left"> Generate hydrogen bonds. </td> <tr> <td align="left"> <a href="ign.html"> IGN </a> </td> <td align="left"> IGNORE </td> <td align="left"> Ignore (this command does nothing). </td> <tr> <td align="left"> <a href="lab.html"> LAB </a> </td> <td align="left"> LABELS </td> <td align="left"> Show labels. </td> <tr> <td align="left"> <a href="loa.html"> LOA </a> </td> <td align="left"> LOAD </td> <td align="left"> Load the specified file. </td> <tr> <td align="left"> <a href="log.html"> LOG </a> </td> <td align="left"> LOG </td> <td align="left"> Write commands to log file. </td> <tr> <td align="left"> <a href="mem.html"> MEM </a> </td> <td align="left"> MEMBRANE </td> <td align="left"> Membrane manipulation. </td> <tr> <td align="left"> <a href="mon.html"> MON </a> </td> <td align="left"> MONO </td> <td align="left"> Switch to mono mode. </td> <tr> <td align="left"> <a href="mov.html"> MOV </a> </td> <td align="left"> MOVE </td> <td align="left"> Define which object should be moved. </td> <tr> <td align="left"> <a href="nei.html"> NEI </a> </td> <td align="left"> NEIGHBORHOOD </td> <td align="left"> Show or hide the sequence neighborhood. </td> <tr> <td align="left"> <a href="pat.html"> PAT </a> </td> <td align="left"> PATTERN </td> <td align="left"> Define sequence pattern. </td> <tr> <td align="left"> <a href="pau.html"> PAU </a> </td> <td align="left"> PAUSE </td> <td align="left"> Pause execution (useful in scripts). </td> <tr> <td align="left"> <a href="pla.html"> PLA </a> </td> <td align="left"> PLANE </td> <td align="left"> Plane manipulation. </td> <tr> <td align="left"> <a href="plo.html"> PLO </a> </td> <td align="left"> PLOT </td> <td align="left"> Plot averaged hydrophob. and/or hydrophobic moment. </td> <tr> <td align="left"> <a href="pos.html"> POS </a> </td> <td align="left"> POSITION </td> <td align="left"> Move structure to specified position. </td> <tr> <td align="left"> <a href="pro.html"> PRO </a> </td> <td align="left"> PROBE </td> <td align="left"> Set the bond probe radius (used to draw nice bonds). </td> <tr> <td align="left"> <a href="exi.html"> QUI </a> </td> <td align="left"> QUIT </td> <td align="left"> The same as exit. </td> <tr> <td align="left"> <a href="rad.html"> RAD </a> </td> <td align="left"> RADIUS </td> <td align="left"> Define sphere radius (used for selection). </td> <tr> <td align="left"> <a href="ram.html"> RAM </a> </td> <td align="left"> RAMACHANDRAN </td> <td align="left"> Draw Ramachandran plot. </td> <tr> <td align="left"> <a href="loa.html"> REA </a> </td> <td align="left"> READ </td> <td align="left"> The same as LOAD. </td> <tr> <td align="left"> <a href="ref.html"> REF </a> </td> <td align="left"> REFRESH </td> <td align="left"> Switch graphics refreshing on or off. </td> <tr> <td align="left"> <a href="reg.html"> REG </a> </td> <td align="left"> REGISTER </td> <td align="left"> Register garlic. </td> <tr> <td align="left"> <a href="rep.html"> REP </a> </td> <td align="left"> REPLACE </td> <td align="left"> Replace selected residues. </td> <tr> <td align="left"> <a href="res.html"> RES </a> </td> <td align="left"> RESTRICT </td> <td align="left"> Restrict current selection. </td> <tr> <td align="left"> <a href="rot.html"> ROT </a> </td> <td align="left"> ROTATE </td> <td align="left"> Rotate structure. </td> <tr> <td align="left"> <a href="sav.html"> SAV </a> </td> <td align="left"> SAVE </td> <td align="left"> Save atomic data to file. </td> <tr> <td align="left"> <a href="sca.html"> SCA </a> </td> <td align="left"> SCALE </td> <td align="left"> Select hydrophobicity scale. </td> <tr> <td align="left"> <a href="sel.html"> SEL </a> </td> <td align="left"> SELECT </td> <td align="left"> Select atoms. </td> <tr> <td align="left"> <a href="seq.html"> SEQ </a> </td> <td align="left"> SEQUENCE </td> <td align="left"> Sequence buffer manipulation. </td> <tr> <td align="left"> <a href="set.html"> SET </a> </td> <td align="left"> SET </td> <td align="left"> Set the specified dihedral angle. </td> <tr> <td align="left"> <a href="sho.html"> SHO </a> </td> <td align="left"> SHOW </td> <td align="left"> Show selected atoms. </td> <tr> <td align="left"> <a href="sla.html"> SLA </a> </td> <td align="left"> SLAB </td> <td align="left"> Change slab style or parameter(s). </td> <tr> <td align="left"> <a href="ssb.html"> SSB </a> </td> <td align="left"> SSB </td> <td align="left"> Change drawing style for disulfide bonds. </td> <tr> <td align="left"> <a href="ste.html"> STE </a> </td> <td align="left"> STEREO </td> <td align="left"> Switch to stereo mode. </td> <tr> <td align="left"> <a href="sti.html"> STI </a> </td> <td align="left"> STICKS </td> <td align="left"> Set the stick radius. </td> <tr> <td align="left"> <a href="str.html"> STR </a> </td> <td align="left"> STRUCTURE </td> <td align="left"> Secondary structure manipulation. </td> <tr> <td align="left"> <a href="tag.html"> TAG </a> </td> <td align="left"> TAG </td> <td align="left"> Assign tag (short text) to structure. </td> <tr> <td align="left"> <a href="cat.html"> TAK </a> </td> <td align="left"> TAKE </td> <td align="left"> The same as CATCH. </td> <tr> <td align="left"> <a href="tbg.html"> TBG </a> </td> <td align="left"> TEXT_BACKGROUND </td> <td align="left"> Change text background color. </td> <tr> <td align="left"> <a href="tfg.html"> TFG </a> </td> <td align="left"> TEXT_FOREGROUND </td> <td align="left"> Check text foreground color. </td> <tr> <td align="left"> <a href="tit.html"> TIT </a> </td> <td align="left"> TITLE </td> <td align="left"> Add title to the main window. </td> <tr> <td align="left"> <a href="tra.html"> TRA </a> </td> <td align="left"> TRANSLATE </td> <td align="left"> Translate structure. </td> <tr> <td align="left"> <a href="ven.html"> VEN </a> </td> <td align="left"> VENN </td> <td align="left"> Draw Venn diagram. </td> <tr> <td align="left"> <a href="whe.html"> WHE </a> </td> <td align="left"> WHEEL </td> <td align="left"> Draw helical wheel. </td> <tr> <td align="left"> <a href="win.html"> WIN </a> </td> <td align="left"> WINDOW </td> <td align="left"> Set sliding window width. </td> </table> <hr size="3"> </html>
