<html> <head> <title> SLA, SLAB </title> </head> <h1 align=center> SLA, SLAB </h1> <hr size="3"> <font color=#880000> <b> NAME <br> </b> </font> SLA, SLAB - change slab. <br><br> <font color=#880000> <b> SYNOPSIS <br> </b> </font> SLA keyword <br> SLA FRONT shift <br> SLA BACK shift <br> SLAB keyword <br> SLAB FRONT shift <br> SLAB BACK shift <br><br> <font color=#880000> <b> DESCRIPTION <br> </b> </font> 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> <font color=#880000> <b> SLAB FRONT shift <br> </b> </font> 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> <font color=#880000> <b> SLAB BACK shift <br> </b> </font> 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> <font color=#880000> <b> SLAB keyword <br> </b> </font> 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> <table border=2 cellspacing=2 cellpading=0> <td align="left"> <font color=#004400> <b> SHORT FORM </b> </font> </td> <td align="left"> <font color=#004400> <b> LONG FORM </b> </font> </td> <td align="left"> <font color=#004400> <b> DESCRIPTION </b> </font> </td> <tr> <td align="left"> OFF </td> <td align="left"> OFF </td> <td align="left"> Switch slab off: all parts <br> of the structure should be visible. <br> </td> <tr> <td align="left"> PLA </td> <td align="left"> PLANE </td> <td align="left"> Use planes as slab surfaces </td> <tr> <td align="left"> SPH </td> <td align="left"> SPHERE </td> <td align="left"> Use spheres as slab surfaces </td> <tr> <td align="left"> CYL </td> <td align="left"> CYLINDER </td> <td align="left"> Use cylinders as slab surfaces </td> <tr> <td align="left"> HALF-SPH </td> <td align="left"> HALF-SPHERE </td> <td align="left"> Use spheres as slab surfaces, but <br> hide the back half of the structure. </td> <tr> <td align="left"> HALF-CYL </td> <td align="left"> HALF-CYLINDER </td> <td align="left"> Use cylinders as slab surfaces, but <br> hide the back half of the structure. </td> </table> <br> 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 user's standpoint). <br><br> <font color=#880000> <b> EXAMPLES <br> </b> </font> <table border=2 cellspacing=2 cellpading=0> <td align="left"> COMMAND </td> <td align="left"> DESCRIPTION </td> <tr> <td align="left"> slab off </td> <td align="left"> Switch slab off </td> <tr> <td align="left"> slab front 4.5 </td> <td align="left"> Move the front slab surface 4.5 angstroms <br> away from the observer </td> <tr> <td align="left"> slab back -2.8 </td> <td align="left"> Move the back slab surface 2.8 angstroms <br> closer to the observer </td> <tr> <td align="left"> slab half-sph </td> <td align="left"> Change slab to semi-spherical </td> </table> <hr size="3"> </html>
