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<div><span></span>Hi everyone,</div><div><br></div><div>I am refining a structure of protein/ligand complex (2.75 <span style="font-family: 'Times New Roman', serif; font-size: 15px; line-height: 22px; background-color: window;">Å</span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">) almost to the last stage. However, I found that some atoms of the ligand is too close to the protein (1.2 or 1.3 </span><span style="font-family: 'Times New Roman', serif; font-size: 11pt; line-height: 1.5; background-color: window;">Å</span><span style="font-size: 10.5pt; line-height: 1.5; background-color: window;">) after refinement.</span></div><div>How should I avoid this? Should I use the "<span style="line-height: normal;">nonbonded_distance_cutoff</span>" parameter? What the value should be set to?</div><div><br></div><div>Another question is that at this resolution is it possible for me to refine the occupancy?</div><div><br></div><div><span style="background-color: rgba(0, 0, 0, 0);">Any suggestion is appreciated.</span></div><div><span style="background-color: rgba(0, 0, 0, 0);"><br></span></div><div><span style="background-color: rgba(0, 0, 0, 0);">Best</span></div><div><span style="background-color: rgba(0, 0, 0, 0);">Xinghua</span></div>
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<div><span><div style="MARGIN: 10px; FONT-FAMILY: verdana; FONT-SIZE: 10pt"><p style="font-family: Arial; font-size: 14px; line-height: 23.799999237060547px; margin: 0cm 0cm 0pt;"><span style="font-family: Verdana; font-size: 10pt; line-height: 1.5; background-color: window;">Xinghua Qin Ph.D</span></p><span style="font-family: Arial;"><p style="margin: 0cm 0cm 0pt;"><span lang="EN-US" style="font-family: Verdana;">Department of Physiology<br>The Fourth Military Medical University<br>169# Changlexi Road<br>Xi'an 710032, China<br>Tel. 86-29-84772779</span></p><p style="margin: 0cm 0cm 0pt;"><span lang="EN-US" style="font-family: Verdana;">E-mail: <a href="mailto:xinghuaqin@126.com" target="_blank" style="color: rgb(0, 0, 0);"><em>xinghuaqin@126.com</em></a></span></p></span></div></span></div>
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