<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="">Hi,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Thanks for the suggested code change; I’ve added it.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Usually when adjusting a bond angle, the bonds aren’t collinear, so it’s easy to choose the axis to rotate around — it’s just the cross product of the two bond vectors. For collinear bonds, like in your line polymer, Chimera chooses an arbitrary axis to rotate around. It just so happens that arbitrary axis it choose was the X axis — exactly the axis that your polymer was lying on! So, the rotation didn’t do anything. If your linear polymer had been in any other direction, it would have worked! Anyway, I’ve now changed the code to check whether the collinear bonds lie on the X axis and if they do then choose a different rotation axis.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Both changes will be in the next daily build and release candidate.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Jun 30, 2016, at 1:44 AM, Jiying Jia <<a href="mailto:jiajiyingxibei@gmail.com" class="">jiajiyingxibei@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi, <div class="">I'm trying to use chimera to adjust angles in my polymer.</div><div class="">First: Probably I found a bug: when I typed "adjust angle 90 #0:4@C #0:5@C #0:6@C" in the command line, it reported that "the degree should be a number". After I changed line 488 in /Chimera/share/Midas/midas_text.py to "degrees, spec = args.split(None,1)", the command works.</div><div class=""><br class=""></div><div class="">Second: still about "adjust angle", if the polymer is a straight line, the command doesn't work, while it works for a random distributed polymer. For the line polymer, type "adjust angle 90 #0:4@C #0:5@C #0:6@C" and then "angle #0:4@C #0:5@C #0:6@C", it returns 180 degree.</div><div class=""><br class=""></div><div class="">Below is the pdb example:</div><div class="">line polymer:</div><div class=""><div class="">ATOM 1 C DA 1 0.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 2 C DA 2 1.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 3 C DA 3 2.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 4 C DA 4 3.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 5 C DA 5 4.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 6 C DA 6 5.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 7 C DA 7 6.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 8 C DA 8 7.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 9 C DA 9 8.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 10 C DA 10 9.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 11 C DA 11 10.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 12 C DA 12 11.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 13 C DA 13 12.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 14 C DA 14 13.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 15 C DA 15 14.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 16 C DA 16 15.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 17 C DA 17 16.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 18 C DA 18 17.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 19 C DA 19 18.000 0.000 0.000 1.00 0.00 C</div><div class="">ATOM 20 C DA 20 19.000 0.000 0.000 1.00 0.00 C</div><div class="">CONECT 1 2</div><div class="">CONECT 2 1 3</div><div class="">CONECT 3 2 4</div><div class="">CONECT 4 3 5</div><div class="">CONECT 5 4 6</div><div class="">CONECT 6 5 7</div><div class="">CONECT 7 6 8</div><div class="">CONECT 8 7 9</div><div class="">CONECT 9 8 10</div><div class="">CONECT 10 9 11</div><div class="">CONECT 11 10 12</div><div class="">CONECT 12 11 13</div><div class="">CONECT 13 12 14</div><div class="">CONECT 14 13 15</div><div class="">CONECT 15 14 16</div><div class="">CONECT 16 15 17</div><div class="">CONECT 17 16 18</div><div class="">CONECT 18 17 19</div><div class="">CONECT 19 18 20</div><div class="">CONECT 20 19</div><div class="">END</div></div><div class="">random polymer:</div><div class=""><div class="">ATOM 1 C DA 1 -7.600 -3.500 -1.800 1.00 0.00 C</div><div class="">ATOM 2 C DA 2 -6.600 -4.500 0.200 1.00 0.00 C</div><div class="">ATOM 3 C DA 3 -3.600 -2.500 -0.800 1.00 0.00 C</div><div class="">ATOM 4 C DA 4 -3.600 -2.500 -1.800 1.00 0.00 C</div><div class="">ATOM 5 C DA 5 -3.600 -2.500 -2.800 1.00 0.00 C</div><div class="">ATOM 6 C DA 6 -3.600 -2.500 -3.800 1.00 0.00 C</div><div class="">ATOM 7 C DA 7 -3.600 -2.500 -4.800 1.00 0.00 C</div><div class="">ATOM 8 C DA 8 -1.600 3.500 -2.800 1.00 0.00 C</div><div class="">ATOM 9 C DA 9 0.400 3.500 -3.800 1.00 0.00 C</div><div class="">ATOM 10 C DA 10 -0.600 0.500 -3.800 1.00 0.00 C</div><div class="">ATOM 11 C DA 11 -1.600 1.500 -1.800 1.00 0.00 C</div><div class="">ATOM 12 C DA 12 -0.600 0.500 0.200 1.00 0.00 C</div><div class="">ATOM 13 C DA 13 -1.600 2.500 2.200 1.00 0.00 C</div><div class="">ATOM 14 C DA 14 1.400 2.500 2.200 1.00 0.00 C</div><div class="">ATOM 15 C DA 15 2.400 0.500 4.200 1.00 0.00 C</div><div class="">ATOM 16 C DA 16 5.400 0.500 4.200 1.00 0.00 C</div><div class="">ATOM 17 C DA 17 6.400 1.500 2.200 1.00 0.00 C</div><div class="">ATOM 18 C DA 18 7.400 -1.500 2.200 1.00 0.00 C</div><div class="">ATOM 19 C DA 19 7.400 -1.500 5.200 1.00 0.00 C</div><div class="">ATOM 20 C DA 20 9.400 -0.500 6.200 1.00 0.00 C</div><div class="">CONECT 1 2</div><div class="">CONECT 2 1 3</div><div class="">CONECT 3 2 4</div><div class="">CONECT 4 3 5</div><div class="">CONECT 5 4 6</div><div class="">CONECT 6 5 7</div><div class="">CONECT 7 6 8</div><div class="">CONECT 8 7 9</div><div class="">CONECT 9 8 10</div><div class="">CONECT 10 9 11</div><div class="">CONECT 11 10 12</div><div class="">CONECT 12 11 13</div><div class="">CONECT 13 12 14</div><div class="">CONECT 14 13 15</div><div class="">CONECT 15 14 16</div><div class="">CONECT 16 15 17</div><div class="">CONECT 17 16 18</div><div class="">CONECT 18 17 19</div><div class="">CONECT 19 18 20</div><div class="">CONECT 20 19</div><div class="">END</div></div><div class=""><br class=""></div><div class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">------------------</div><div class="">Best Wishes!</div><div class="">Jiying Jia</div></div></div></div></div></div>
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