<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Jiying Jia,<div>The “findclash” default is to ignore interactions between atoms that are separated by 4 or fewer bonds, and this is controlled by the “bondSeparation” option. For example, to ignore only interactions between pairs of atoms that are directly bonded (separated by 1 bond), you would use a command something like:</div><div><br></div><div>findclash #0 test #0 bondSep 1</div><div><br></div><div>… giving results shown in attached image, except I changed the line colors afterwards.</div><div><br></div><div>You can use command “help findclash” to see the findclash manual page (which explains the options and their default values), or see it on our website here:</div><div><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html</a>></div><div><br></div><div>I hope this helps,</div><div>Elaine<br><div>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br><br></div><div><img height="210" width="300" apple-width="yes" apple-height="yes" apple-inline="yes" id="8994FA78-A183-4E4B-8B1E-40517D648C96" src="cid:A21ED61C-FC7A-4F8C-8958-8FC7ACFE347C@gateway.sonic.net"></div>On Jul 6, 2016, at 6:38 AM, xibei <<a href="mailto:zhuceyonghu123@126.com">zhuceyonghu123@126.com</a>> wrote:<br><br><blockquote type="cite">Hi,<br>I'm trying to use command "findclash" to check the excluded volume effect by detecting overlaps between atoms. The command I use is "findclash #0 test #0" or "findclash #0 overlapCutoff value test #0", but I found that two close atoms (14C,16C, dis=0.8) are not identified as "overlaped" while another two atoms (11C, 16C, dis=1.8) whose distance is larger are overlaped... Is there anything wrong about understanding the overlap?<br><br>Example molecular (init.mol2):<br>@<TRIPOS>MOLECULE<br>init.mol2<br>20 19 20 0 0<br>NUCLEIC_ACID<br>NO_CHARGES<br><br><br>@<TRIPOS>ATOM<br> 1 C 14.7888 10.0072 -5.6663 C.3 1 DA 0.0000<br> 2 C 15.4013 8.5150 -3.5012 C.3 2 DA 0.0000<br> 3 C 13.7388 8.7698 -5.6133 C.3 3 DA 0.0000<br> 4 C 14.6414 7.5770 -3.3654 C.3 4 DA 0.0000<br> 5 C 12.9675 5.9273 -2.0359 C.3 5 DA 0.0000<br> 6 C 13.6457 4.0155 -0.2544 C.3 6 DA 0.0000<br> 7 C 12.8822 2.8588 2.0634 C.3 7 DA 0.0000<br> 8 C 11.7541 3.3958 4.4562 C.3 8 DA 0.0000<br> 9 C 11.2290 4.5854 6.8231 C.3 9 DA 0.0000<br> 10 C 13.8907 4.6510 7.2730 C.3 10 DA 0.0000<br> 11 C 15.5581 5.2490 9.3114 C.3 11 DA 0.0000<br> 12 C 17.8150 4.7800 10.7177 C.3 12 DA 0.0000<br> 13 C 18.0666 2.1205 10.3271 C.3 13 DA 0.0000<br> 14 C 16.9288 4.4119 9.4640 C.3 14 DA 0.0000<br> 15 C 14.9471 3.0788 10.7232 C.3 15 DA 0.0000<br> 16 C 16.7345 3.9070 8.8773 C.3 16 DA 0.0000<br> 17 C 15.5384 2.3512 10.7314 C.3 17 DA 0.0000<br> 18 C 16.0476 1.4159 8.2501 C.3 18 DA 0.0000<br> 19 C 17.5152 1.5369 5.9877 C.3 19 DA 0.0000<br> 20 C 17.5650 3.1811 3.8468 C.3 20 DA 0.0000<br>@<TRIPOS>BOND<br> 1 1 2 1<br> 2 2 3 1<br> 3 3 4 1<br> 4 4 5 1<br> 5 5 6 1<br> 6 6 7 1<br> 7 7 8 1<br> 8 8 9 1<br> 9 9 10 1<br> 10 10 11 1<br> 11 11 12 1<br> 12 12 13 1<br> 13 13 14 1<br> 14 14 15 1<br> 15 15 16 1<br> 16 16 17 1<br> 17 17 18 1<br> 18 18 19 1<br> 19 19 20 1<br>@<TRIPOS>SUBSTRUCTURE<br> 1 DA 1 RESIDUE 4 A DA 1 ROOT<br> 2 DA 2 RESIDUE 4 A DA 2<br> 3 DA 3 RESIDUE 4 A DA 2<br> 4 DA 4 RESIDUE 4 A DA 2<br> 5 DA 5 RESIDUE 4 A DA 2<br> 6 DA 6 RESIDUE 4 A DA 2<br> 7 DA 7 RESIDUE 4 A DA 2<br> 8 DA 8 RESIDUE 4 A DA 2<br> 9 DA 9 RESIDUE 4 A DA 2<br> 10 DA 10 RESIDUE 4 A DA 2<br> 11 DA 11 RESIDUE 4 A DA 2<br> 12 DA 12 RESIDUE 4 A DA 2<br> 13 DA 13 RESIDUE 4 A DA 2<br> 14 DA 14 RESIDUE 4 A DA 2<br> 15 DA 15 RESIDUE 4 A DA 2<br> 16 DA 16 RESIDUE 4 A DA 2<br> 17 DA 17 RESIDUE 4 A DA 2<br> 18 DA 18 RESIDUE 4 A DA 2<br> 19 DA 19 RESIDUE 4 A DA 2<br> 20 DA 20 RESIDUE 4 A DA 1<br><br>Best Wishes!<br>Jiying Jia<br></blockquote><br></div></body></html>