<HTML> <HEAD> <TITLE> SLA, SLAB </TITLE> </HEAD> <BODY BACKGROUND="garlic.gif"> <FONT FACE="Times, Helvetica"> <H1 ALIGN=CENTER> <FONT SIZE=5> <B> SLA, SLAB </B> </FONT> </H1> <HR SIZE="3"> <FONT SIZE=3 COLOR=#880000> <B> NAME <BR> </B> </FONT> <FONT SIZE=2> <B> SLA, SLAB - change slab. <BR><BR> </B> </FONT> <FONT SIZE=3 COLOR=#880000> <B> SYNOPSIS <BR> </B> </FONT> <FONT SIZE=2> <B> SLA keyword <BR> SLA FRONT shift <BR> SLA BACK shift <BR> SLAB keyword <BR> SLAB FRONT shift <BR> SLAB BACK shift <BR><BR> </B> </FONT> <FONT SIZE=3 COLOR=#880000> <B> DESCRIPTION <BR> </B> </FONT> <FONT SIZE=2> <B> Change the slab. Slab is used to cut the slice out from the structure and to hide the rest. Two slab surfaces are used: the front slab surface, which is the one closer to the observer and the back slab surface. There are three versions of this command: <BR><BR> (1) SLAB FRONT shift ----> move the front slab surface; <BR> (2) SLAB BACK shift ----> move the back slab surface; <BR> (3) SLAB keyword ----> switch slab off or change the type of the surfaces. <BR><BR> </B> </FONT> <FONT SIZE=3 COLOR=#880000> <B> SLAB FRONT shift <BR> </B> </FONT> <FONT SIZE=2> <B> This command moves the front slab surface. It is recommended to use this command in scripts - in interactive mode, use controls (keys DEL and ENTER on numeric keypad). The shift value should be given in angstroms. Positive shift moves the front slab surface away from the observer. FRONT may be abbreviated to FRO. <BR><BR> </B> </FONT> <FONT SIZE=3 COLOR=#880000> <B> SLAB BACK shift <BR> </B> </FONT> <FONT SIZE=2> <B> This command moves the back slab surface. It is recommended to use this command in scripts - in interactive mode, use controls (keys 1 and 3 on the numeric keypad). The shift value should be given in angstroms. Positive shift moves the back slab surface away from the observer. BACK may be abbreviated to BAC. <BR><BR> </B> </FONT> <FONT SIZE=3 COLOR=#880000> <B> SLAB keyword <BR> </B> </FONT> <FONT SIZE=2> <B> Some keywords may be used to change the type of slab surfaces and to switch slab off. Here is the list of keywords: <BR><BR> </B> </FONT> <TABLE BORDER=2 CELLSPACING=2 CELLPADING=0> <TD ALIGN="left"> <FONT SIZE=2> <B> SHORT FORM </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> LONG FORM </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> DESCRIPTION </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> OFF </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> OFF </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Switch slab off: all parts <BR> of the structure should be visible. <BR> </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> PLA </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> PLANE </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Use planes as slab surfaces </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> SPH </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> SPHERE </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Use spheres as slab surfaces </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> CYL </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> CYLINDER </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Use cylinders as slab surfaces </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> HALF-SPH </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> HALF-SPHERE </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Use spheres as slab surfaces, but <BR> hide the back half of the structure. </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> HALF-CYL </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> HALF-CYLINDER </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Use cylinders as slab surfaces, but <BR> hide the back half of the structure. </B> </FONT> </TD> </TABLE> <BR> <FONT SIZE=2> <B> For most structures, the planar slab is the best choice. Spherical and semi-spherical slab may be useful when working with large globular proteins, while cylindrical and semi-cylindrical slab is useful when working with beta-barrel proteins (like porins). The cylinder axis is parallel to y axis (vertical from users standpoint). <BR><BR> </B> </FONT> <FONT SIZE=3 COLOR=#880000> <B> EXAMPLES <BR> </B> </FONT> <TABLE BORDER=2 CELLSPACING=2 CELLPADING=0> <TD ALIGN="left"> <FONT SIZE=2> <B> COMMAND </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> DESCRIPTION </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> slab off </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Switch slab off </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> slab front 4.5 </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Move the front slab surface 4.5 angstroms <BR> away from the observer </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> slab back -2.8 </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Move the back slab surface 2.8 angstroms <BR> closer to the observer </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> slab half-sph </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Change slab to semi-spherical </B> </FONT> </TD> </TABLE> <HR SIZE="3"> </FONT> </BODY> </HTML>
