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<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">Hello<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">I want to find H-bonds between 3 residues and the ligand and the water molecules around the ligand in 3 angstrom, but I don’t want H-bonds between water molecules. I Just want h-bonds between residues together and residues with ligand and residues and ligand with water. I have used Per-Frame script system. But I have two problems. First, if I set selection mode on replace mode and write this script:<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">*********************<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">~display :SOL<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">zonesel :279 3 :SOL<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">select up<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">display sel<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">select :38:53:147:279<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">findhbond linewidth 3 color blue selRestrict :SOL:38:53:147:279<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">*********************<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">The result is fine and H-bonds that I want were display. But if I apply this script, the system searches every water residues for find H-bond and take a lot of time per frame.<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">second, if I set selection mode on append and write this script:<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">*********************<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">~display :SOL<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">zonesel :279 3 :SOL<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">select up<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">display sel<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">select :38:53:147:279<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">findhbond linewidth 3 color blue selRestrict both<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">*********************<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">The calculations are going faster, but also, show H-bonds between water molecules with themselves that I don’t want it.<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">How can I hide H-bonds between water molecule with themselves but H-bonds between selected residues and ligand and water retain?<span></span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%"><span> </span></span></p>

<p class="MsoNormal" style="margin:0in 0in 8pt;line-height:107%;font-size:11pt;font-family:"Calibri",sans-serif"><span style="font-size:14pt;line-height:107%">Thank you, everyone,</span><span dir="RTL" style="font-size:14pt;line-height:107%;font-family:"Arial",sans-serif" lang="FA"><span></span></span></p>





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