<html> <head> <title> ATO, ATOMS </title> </head> <h1 align=center> ATO, ATOMS </h1> <hr size="3"> <font color=#880000> <b> NAME <br> </b> </font> ATO, ATOMS - change drawing style for atoms. <br><br> <font color=#880000> <b> SYNOPSIS <br> </b> </font> ATO style <br> ATOMS style <br><br> <font color=#880000> <b> DESCRIPTION <br> </b> </font> Change drawing style for atoms. Atom style is defined separately from bond style. For BALLS, BA2, BIG, BI2, COVALENT, CO2, SMALL, SM2, SPACEFILL and SP2 style, atomic radii are read from .garlicrc file. If this file is not available, hard-coded defaults are used. The styles listed above may be used to produce nice output but require more CPU time than other styles. The list of realistic, nice styles, sorted by size, from the smallest to the largest: <br> (1) SMALL and SM2; <br> (2) COVALENT and CO2; <br> (3) SPACEFILL and SP2; <br> (4) BIG and BI2. <br><br> Note that BALLS and BA2 style are not included in this list. All atoms drawn using this style will have the same physical size. <br><br> The second version of a given style has more enhanced contrast and more specular look than the first version (BA2 vs. BALL, BI2 vs. BIG etc). See the image at the bottom of this page to understand this difference. <br><br> <table border=2 cellspacing=2 cellpading=0> <td align="left"> STYLE </td> <td align="left"> DESCRIPTION </td> <td align="left"> size </td> <tr> <td align="left"> 0 </td> <td align="left"> Invisible atoms. </td> <td align="left"> Fixed size. </td> <tr> <td align="left"> 1 </td> <td align="left"> A single pixel. </td> <td align="left"> Fixed size. </td> <tr> <td align="left"> 2 </td> <td align="left"> 3x3 cross (5 pixels). </td> <td align="left"> Fixed size. </td> <tr> <td align="left"> 3 </td> <td align="left"> 3x3 square (9 pixels). </td> <td align="left"> Fixed size. </td> <tr> <td align="left"> 4 </td> <td align="left"> 5x5 circle (21 pixel). </td> <td align="left"> Fixed size. </td> <tr> <td align="left"> 5 </td> <td align="left"> 7x7 square (37 pixels). </td> <td align="left"> Fixed size. </td> <tr> <td align="left"> 6 </td> <td align="left"> 9x9 circle (61 pixel). </td> <td align="left"> Fixed size. </td> <tr> <td align="left"> 7 </td> <td align="left"> 11x11 circle (109 pixels). </td> <td align="left"> Fixed size. </td> <tr> <td align="left"> bal <br> balls </td> <td align="left"> Balls (suitable to draw balls and sticks). </td> <td align="left"> Proportional. </td> <tr> <td align="left"> ba2 </td> <td align="left"> Balls with enhanced contrast. </td> <td align="left"> Proportional. </td> <tr> <td align="left"> sma <br> small </td> <td align="left"> Small style (default: 70% of covalent radius). </td> <td align="left"> Proportional. </td> <tr> <td align="left"> sm2 </td> <td align="left"> Small style, enhanced contrast. </td> <td align="left"> Proportional. </td> <tr> <td align="left"> cov <br> covalent </td> <td align="left"> Covalent style (default: covalent radius). </td> <td align="left"> Proportional. </td> <tr> <td align="left"> co2 </td> <td align="left"> Covalent style, enhanced contrast. </td> <td align="left"> Proportional. </td> <tr> <td align="left"> spa <br> spacefill </td> <td align="left"> Spacefill style (default: 70% of van der Waals radius). </td> <td align="left"> Proportional. </td> <tr> <td align="left"> sp2 </td> <td align="left"> Spacefill style, enhanced contrast. </td> <td align="left"> Proportional. </td> <tr> <td align="left"> big </td> <td align="left"> Big style (default: van der Waals radius). </td> <td align="left"> Proportional. </td> <tr> <td align="left"> bi2 </td> <td align="left"> Big style, enhanced contrast. </td> <td align="left"> Proportional. </td> </table> <br> <font color=#880000> <b> EXAMPLES <br> </b> </font> The image below shows all drawing styles for atoms. To reproduce this image, execute the script atoms.script; the file trp.pdb (tryptophan) is required as input. <br><br> <img src="atoms.gif"> <br><br> <font color=#880000> <b> NOTES <br> </b> </font> (1) Invisible atoms (style 0) are not treated as hidden - they are just invisible. <br><br> (2) A good performance and fairly good contrast may be achieved choosing atom drawing style 0 (no pixels) and bond drawing style 2 (line width of three pixels). <br><br> (3) The ATOM keywords SMALL, SM2, COVALENT, CO2, SPACEFILL, SP2, BIG and BI2 may be combined with the command BONDS NICE to produce very nice images. All other atomic styles (0 - 7, BALL, BA2) will not work with BONDS NICE. <br><br> <font color=#880000> <b> RELATED COMMANDS <br> </b> </font> The command BAL (BALLS) is used to change the ball radius. BON (BONDS) is used to change drawing style for bonds. PRO (PROBE) is used to change the bond probe radius (this probe is used to draw nice bonds). <br><br> <hr size="3"> </html>
