<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">My task is to identify ligand interactions with protein residues throughout an MD trajectory. I thought of something along the lines <div class="">sel ligand z<3.5 #for vdW interactions, etc. </div><div class=""><br class=""></div><div class="">I don’t think this can be done using the MD movie interface but I may be wrong.</div><div class=""><br class=""></div><div class="">I then tried the following:</div><div class="">1. sel protein/hold selection steady</div><div class="">2. sel ligand</div><div class="">3. calculate occupancy (MD Movie/Analysis)</div><div class="">4. Chimera/select/clear selection</div><div class="">5. turned the Volume Viewer to mesh/level2.</div><div class=""><br class=""></div><div class="">What I obtained is a mesh grid enclosing solid surfaces (see attached snapshot). I’m not able to get rid of these surfaces? </div><div class=""><br class=""></div><div class="">I think that the problem ma be in step 2 above (sel :ligand). My ligand is N,N-Diethyl-meta-toluamide. Should I select the aromatic ring part separately of the amide part, run the above process and then repeat selecting the amide part? </div><div class=""><div class=""><br class=""></div><div class="">I also tried MD movie/Analysis/Residue interaction network, first selecting the ligand. </div><div class=""><br class=""></div><div class="">The results I obtained are not satisfactory. </div><div class=""><br class=""></div><div class="">Is there a better way of dealing with my problem?</div><div class=""><br class=""></div><div class="">Thanks in advance for your kind help</div><div class=""><br class=""></div><div class="">George</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="1083F989-4755-4019-8D6A-88F77E37F35A" height="295" width="469" apple-width="yes" apple-height="yes" src="cid:3A660C5B-8ACB-4656-B1DD-57DBB2B56C98" class=""> <img apple-inline="yes" id="D38E2C90-992B-4858-BCE9-7F8ACB1598C4" height="452" width="403" apple-width="yes" apple-height="yes" src="cid:49E3D42E-B23E-46DE-A3E8-16CCDBD3D99C" class=""></div></div></body></html>