@text KINEMAGE 1 - Practice at Drawline and rotation In the graphics window you will see an object made of dots with the first few connected. The image is depth-cued, so dots or lines further away will look smaller and less bright. Rotate the image in 3D by dragging slowly back and forth with the mouse. The purpose of this kinemage is for you to practice, so draw in all the rest of the lines to continue the pattern. This kinemages will have the drawline function already turned on. Click on two points to draw a green line between them (you must pick each end of each line). Remember to frequently rotate the visual object by dragging with the mouse, starting someplace that is NOT a point. A summary of these instructions will be in the caption window, and an even briefer reminder is written at the top of the graphics screen. If rotating the image shows you a mistake, you can use "eraselast" as an undo. [Turn on "PickEraseNew" to punch out earlier drawn lines (if several lines meet, you may end up removing an extra one and need to redraw it afterward). Remember to turn "Drawline" back on to continue the test.] Now turn on the "DrawBall" button. Click on the last three points at the green end of the figure to decorate them with purple balls. You will notice that each time you picked (that is, clicked on) a point, the point's identifier was shown at the lower left corner of the graphics screen. Place labels at the first 3 points on the blue end of the graphics object, by selecting the "Labels" button in the panel on the right side of the graphics screen, and picking each of those points in turn. Once you feel comfortable with the rotation and the drawing functions and have read thru at least the next section of these explanations so you know what's coming, go to the "Kinemage" pulldown menu and choose "next" in order to start the 3D molecular literacy test, each part of which is timed. KINEMAGE 2 - Connect-the-atoms Exercise The first thing that comes up is a dialog box requesting a unique personal identifier for you: e.g. a short form of your name. The results of this timed test will be put into a file named with some characters of the original file name, some characters of your personal identifier, a time-stamp number, and then .kin for the file type. (Some systems restrict file name length to 31 characters.) Once you have entered your name, the timer will start counting down. What you see is a separate white dot for each atom in this small piece of protein structure. Use Drawline to connect atoms that are covalently bonded (i.e., suitably close together in 3D) - you draw a line by clicking on each end of it. Both backbone and sidechains are included, but not H atoms. Drag with the mouse slowly from side to side in order to see the atom dots in 3D. Turning the structure around will let you identify protruding side chains as a starting point for drawing in the bonds. This kinemage will have the drawline function already turned on. Click on two points to draw a green line between them (you must pick each end of each line). Tip: when you pick an atom its element type will be shown, and when you connect to the next atom the distance between them in Angstroms will be shown. If you make an incorrect bond, use "Eraselast" to take that last one away, or invoke "PickEraseNew" to punch out any of your drawn lines (remember to turn "Drawline" back on to continue the test). When the timer reaches zero, a dialog box will come up to save your work (you may need to move the mouse to wake it up). Your name and a time-stamp should already be part of the output file name. Read the brief summary of the exercise to come, then click the "OK" button, which will automatically start the next part of the test (also timed). KINEMAGE 3 - Label-particular-geometry exercise: This kinemage shows backbone in white and sidechains in cyan, from a small piece of protein structure with all of the sidechains branched. The object of the exercise is to distinguish the type of geometry at branch points in protein sidechains. Some branch points are planar: that is, constrained to have only 3 covalently bonded neighbors all in the same plane which includes the central atom (sp2 hybridization for you chemists). Other branch points have tetrahedral geometry (sp3), where the 3 bonded non-H neighbors are symmetrically placed but strongly non-planar with the central atom. The task is to label each atom that is a sidechain tetrahedral branch point. Atom types and residue names are not given, so you must distinguish tetrahedral from planar branches just from their 3D geometry. Label just one branch-point per sidechain, and do not label any backbone atoms. Click on the atom to select and label it. Remember the "eraselast" button to remove the last one made, or "PickEraseNew" to remove any one you decide was a mistake. NOTE: the picking-point of a label is the lower-left corner of the first character (which may be a space)! (The "w" key toggles label-character size) The timer will show the time left; when it reaches zero, a dialog box will come up to save your work. (Your name and a time-stamp should already be part of the output file name.) Read the brief instructions for the next part. Then click the "OK" button to accept the output, and you will start in the next timed kinemage exercise. KINEMAGE 4 - Identify-particular-types-of-atoms exercise: This kinemage shows both backbone and sidechains in white, for a short peptide. The task in this exercise is to identify all the backbone Oxygen atoms in this piece of structure by placing balls on them. (Do not mark any sidechain atoms.) Click on an atom to select and place a ball on it. Remember the "eraselast" button to remove the last made one, or "PickEraseNew" to remove any one you decide was a mistake. When the timer reaches zero, a dialog box will save your work. (Your name and a time-stamp should already be part of the output file name.) Read the brief instructions for the next part. Then click the "OK" button to accept the output, and you will start in the next timed kinemage exercise (or exit the program after the last timed exercise). KINEMAGE 5 - Find-the-interactions exercise: This kinemage shows the backbone (in white) and the sidechains (in cyan), for a small piece out of a protein structure. Find a good view, and choose "Set Reader's View" on the Views pulldown menu so you can get back to it. The object of the exercise is to find the hydrogen bonds and draw them in. This kinemage has the drawline function already turned on. Click on two atoms to draw a green line between them, which will be shortened for less confusion with the covalent bonds. (If you uncheck the drawline button temporarily, you can take advantage of the atom-identity and distance displays at the bottom of the screen, without producing any new lines.) Now start looking for possible donor-acceptor pairs on the backbone, with suitable geometry. When you find one, draw in the H-bond. (If you don't like it, once you move it around and look from all angles, then remove it with the "eraselast" button.) Once you have drawn lines for all the backbone H-bonds, see if you can find any sidechain-to-backbone or sidechain-sidechain H-bonds and draw them in also, again checking for rsuitable geometry. When the timer reaches zero, a dialog box will come up to save your work. (Your name and a time-stamp should already be part of the output file name.) Click the "OK" button to accept the output, and then you will exit the program. @kinemage 1 @caption Practice, for rotating image and drawing lines: Draw lines between adjacent points to continue the pattern. Then put balls on the last 3 points at the green end; then label the first 3 points at the blue end. @drawline @drawlabel @drawball @nosavealert @bigfonts @viewid {} @zoom 1.00 @zslab 200 @ztran 0 @center 14.362 -5.802 -14.769 @matrix 0.88797 -0.29127 0.35590 0.02085 0.79857 0.60155 -0.45942 -0.52674 0.71518 @group {object} dominant @dotlist {skein} {ultimate} P 16.727, -0.149, -11.257 {penultimate} L 17.487, -1.063, -12.184 {antepenultimate} L 17.919, -2.571, -12.122 {R4 } L 17.344, -3.840, -11.489 {R5 } L 15.872, -4.396, -10.940 {R6 } L 14.390, -4.170, -11.310 {R7 } L 13.562, -3.579, -12.643 {R8 } L 13.761, -3.486, -14.199 {R9 } L 14.662, -4.240, -15.304 {R10 } L 15.275, -5.639, -15.422 {R11 } L 15.013, -7.143, -14.728 {R12 } L 13.753, -7.924, -14.093 {R13 } L 12.010, -7.818, -14.133 {R14 } L 10.887, -7.342, -15.143 {R15 } L 10.805, -7.090, -16.784 {R16 } L 11.461, -7.669, -18.106 {R17 } L 12.224, -9.036, -18.598 {R18 } L 12.200, -10.494, -18.236 {R19 } L 11.185, -11.454, -17.505 @vectorlist {skein} color= sky {ultimate} P 16.727, -0.149, -11.257 {penultimate} L 17.487, -1.063, -12.184 {antepenultimate} L 17.919, -2.571, -12.122 {R4} L 17.344, -3.840, -11.489 {R5} L 15.872, -4.396, -10.940 @labellist {instructions} screen {Connect the dots to complete the figure} -180, 180, 100 @group {answer} dominant nobutton off @vectorlist {skein} answer {R5 asp 4 14 } 15.872, -4.396, -10.940 {R6 ala 4 15 } L 14.390, -4.170, -11.310 {R7 ala 4 15 } L 13.562, -3.579, -12.643 {R8 arg 4 16 } L 13.761, -3.486, -14.199 {R9 arg 4 16 } L 14.662, -4.240, -15.304 {R10arg 4 17 } L 15.275, -5.639, -15.422 {R11arg 4 17 } L 15.013, -7.143, -14.728 {R12leu 4 18 } L 13.753, -7.924, -14.093 {R13leu 4 18 } L 12.010, -7.818, -14.133 {R14lys 4 19 } L 10.887, -7.342, -15.143 {R15lys 4 19 } L 10.805, -7.090, -16.784 {R16ala 4 20 } L 11.461, -7.669, -18.106 {R17ala 4 20 } L 12.224, -9.036, -18.598 {R18ile 4 21 } L 12.200, -10.494, -18.236 {R19ile 4 21 } L 11.185, -11.454, -17.505 @kinemage 2 @caption For this next exercise: Connect the dots, by drawing lines to join all and only the covalently-bonded atom pairs in this short single peptide. (H atoms not shown.) @bigfonts @minutes 5.0 @drawline @zoom 1.10 @zslab 200 @ztran 0 @center 12.724 20.620 38.028 @matrix 0.731057 0.027287 0.681770 0.077658 0.989380 -0.122871 -0.677883 0.142771 0.721175 @group {molecule} dominant @dotlist {mc} color= white { n} 13.040 17.795 41.576 { c}12.857 18.149 40.184 { c}14.114 18.008 39.316 { o}14.048 17.888 38.093 { n}15.305 17.864 39.973 { c}16.535 17.608 39.135 { c}16.402 16.224 38.477 { o}17.056 16.011 37.442 { n}15.583 15.317 39.042 { c}15.499 13.975 38.423 { c}14.809 13.994 37.122 { o}14.895 13.025 36.369 { n}14.042 15.099 36.779 { c}13.446 15.223 35.447 { c}14.119 16.379 34.699 { o}13.596 16.797 33.677 { n}15.263 16.821 35.188 { c}16.013 17.930 34.575 { c}15.165 19.224 34.608 { o}15.256 20.030 33.643 { n}14.447 19.374 35.690 { c}13.541 20.571 35.732 { c}14.333 21.829 35.972 { o}15.432 21.828 36.597 { n}13.746 22.917 35.515 { c}14.428 24.253 35.706 { c}14.072 24.838 37.046 { o}14.814 25.675 37.588 { n}12.962 24.437 37.624 { c}12.455 24.918 38.860 { c}11.270 24.038 39.309 { o}11.166 22.934 38.745 { n}10.468 24.477 40.220 { c}9.341 23.677 40.724 { c}8.014 24.056 40.127 { o}6.945 23.901 40.752 { o}8.007 24.586 38.911 @dotlist {sc} color= white { c}12.233 19.507 39.987 { c}13.095 20.671 40.457 { c}14.194 21.065 39.681 { c}14.934 22.214 40.058 { c}14.461 22.849 41.215 { o}15.100 24.043 41.591 { c}12.583 21.401 41.536 { c}13.326 22.521 41.917 { c} L 17.807, 17.687, 39.982 { c} L 18.137, 19.055, 40.582 { c} L 19.351, 18.961, 41.495 { c} L 18.443, 20.064, 39.487 { c}14.835 13.011 39.441 { c}11.959 15.380 35.423 { c}11.340 16.558 36.137 { c}11.215 17.839 35.598 { n}10.523 18.632 36.528 { c}10.220 17.870 37.574 { c}10.716 16.565 37.369 { c}9.563 18.166 38.739 { c}9.443 17.229 39.763 { c}10.589 15.591 38.379 { c}9.882 15.917 39.547 { c} L 16.411, 17.589, 33.138 { c} L 16.747, 16.123, 32.918 { s} L 18.212, 15.601, 33.827 { c} L 19.416, 16.792, 33.244 { c} L 14.046, 25.251, 34.597 { o} L 14.539, 24.781, 33.337 { c} L 14.646, 26.620, 34.881 { c}12.014 26.385 38.791 { c}11.007 26.601 37.706 { o}10.255 25.646 37.258 { n}10.855 27.812 37.187 { c}9.319 23.646 42.224 { c}9.108 24.999 42.940 { o}8.905 26.015 42.191 { o}8.936 24.955 44.136 @labellist {instr} color= white screen {Connect the covalently-bonded atom pairs} -180 180 100 @group {ref} dominant nobutton off @vectorlistlist {bonds} color= green answer { n tyr 65 } <1ammH65_73 mut> P 13.040 17.795 41.576 { ca tyr 65 }12.857 18.149 40.184 { c tyr 65 }14.114 18.008 39.316 { o tyr 65 }14.048 17.888 38.093 { c tyr 65 }P 14.114 18.008 39.316 { n leu 66 }15.305 17.864 39.973 { ca leu 66 } L 16.535, 17.608, 39.135 { c leu 66 } L 16.402, 16.224, 38.477 { o leu 66 } L 17.056, 16.011, 37.442 { c leu 66 } P 16.402, 16.224, 38.477 { n ala 67 }15.583 15.317 39.042 { ca ala 67 }15.499 13.975 38.423 { c ala 67 }14.809 13.994 37.122 { o ala 67 }14.895 13.025 36.369 { c ala 67 }P 14.809 13.994 37.122 { n trp 68 }14.042 15.099 36.779 { ca trp 68 }13.446 15.223 35.447 { c trp 68 }14.119 16.379 34.699 { o trp 68 }13.596 16.797 33.677 { c trp 68 }P 14.119 16.379 34.699 { n met 69 }15.263 16.821 35.188 { ca met 69 }16.013 17.930 34.575 { c met 69 }15.165 19.224 34.608 { o met 69 }15.256 20.030 33.643 { c met 69 }P 15.165 19.224 34.608 { n gly 70 }14.447 19.374 35.690 { ca gly 70 }13.541 20.571 35.732 { c gly 70 }14.333 21.829 35.972 { o gly 70 }15.432 21.828 36.597 { c gly 70 }P 14.333 21.829 35.972 { n thr 71 } L 13.746, 22.917, 35.515 { ca thr 71 } L 14.428, 24.253, 35.706 { c thr 71 } L 14.072, 24.838, 37.046 { o thr 71 } L 14.814, 25.675, 37.588 { c thr 71 } P 14.072, 24.838, 37.046 { n asn 72 }12.962 24.437 37.624 { ca asn 72 }12.455 24.918 38.860 { c asn 72 }11.270 24.038 39.309 { o asn 72 }11.166 22.934 38.745 { c asn 72 }P 11.270 24.038 39.309 { n asp 73 }10.468 24.477 40.220 { ca asp 73 }9.341 23.677 40.724 { c asp 73 }8.014 24.056 40.127 { o asp 73 }6.945 23.901 40.752 { c asp 73 }P 8.014 24.056 40.127 { n ser 74 }8.007 24.586 38.911 { ca tyr 65 }P 12.857 18.149 40.184 { cb tyr 65 }12.233 19.507 39.987 { cg tyr 65 }13.095 20.671 40.457 { cd1 tyr 65 }14.194 21.065 39.681 { ce1 tyr 65 }14.934 22.214 40.058 { cz tyr 65 }14.461 22.849 41.215 { oh tyr 65 }15.100 24.043 41.591 { cg tyr 65 }P 13.095 20.671 40.457 { cd2 tyr 65 }12.583 21.401 41.536 { ce2 tyr 65 }13.326 22.521 41.917 { cz tyr 65 }14.461 22.849 41.215 { ca leu 66 } P 16.535, 17.608, 39.135 { cb leu 66 } L 17.807, 17.687, 39.982 { cg leu 66 } L 18.137, 19.055, 40.582 { cd1 leu 66 } L 19.351, 18.961, 41.495 { cg leu 66 } P 18.137, 19.055, 40.582 { cd2 leu 66 } L 18.443, 20.064, 39.487 { ca ala 67 }P 15.499 13.975 38.423 { cb ala 67 }14.835 13.011 39.441 { ca trp 68 }P 13.446 15.223 35.447 { cb trp 68 }11.959 15.380 35.423 { cg trp 68 }11.340 16.558 36.137 { cd1 trp 68 }11.215 17.839 35.598 { ne1 trp 68 }10.523 18.632 36.528 { ce2 trp 68 }10.220 17.870 37.574 { cg trp 68 }P 11.340 16.558 36.137 { cd2 trp 68 }10.716 16.565 37.369 { ce2 trp 68 }10.220 17.870 37.574 { cz2 trp 68 }9.563 18.166 38.739 { ch2 trp 68 }9.443 17.229 39.763 { cd2 trp 68 }P 10.716 16.565 37.369 { ce3 trp 68 }10.589 15.591 38.379 { cz3 trp 68 }9.882 15.917 39.547 { ch2 trp 68 }9.443 17.229 39.763 { ca met 69 } P 16.013, 17.930, 34.575 { cb met 69 } L 16.411, 17.589, 33.138 { cg met 69 } L 16.747, 16.123, 32.918 { sd met 69 } L 18.212, 15.601, 33.827 { ce met 69 } L 19.416, 16.792, 33.244 { ca thr 71 } P 14.428, 24.253, 35.706 { cb thr 71 } L 14.046, 25.251, 34.597 { og1 thr 71 } L 14.539, 24.781, 33.337 { cb thr 71 } P 14.046, 25.251, 34.597 { cg2 thr 71 } L 14.646, 26.620, 34.881 { ca asn 72 }P 12.455 24.918 38.860 { cb asn 72 }12.014 26.385 38.791 { cg asn 72 }11.007 26.601 37.706 { od1 asn 72 }10.255 25.646 37.258 { cg asn 72 }P 11.007 26.601 37.706 { nd2 asn 72 }10.855 27.812 37.187 { ca asp 73 }P 9.341 23.677 40.724 { cb asp 73 }9.319 23.646 42.224 { cg asp 73 }9.108 24.999 42.940 { od1 asp 73 }8.905 26.015 42.191 { cg asp 73 }P 9.108 24.999 42.940 { od2 asp 73 }8.936 24.955 44.136 @kinemage 3 @caption In this next exercise: For each of these branched sidechains, label the atom at the branch point if its geometry is tetrahedral (=sp3). Do not label atoms with planar geometry, or backbone atoms. @minutes 1.5 @drawlabel @bigfonts @zoom 1.00 @zslab 180 @center 15.158 -8.667 49.774 @matrix -0.116978 -0.960285 -0.253319 0.721624 -0.257431 0.642642 -0.682330 -0.107626 0.723078 @master {mainchain} @master {Hbonds} @master {sidechain} @group {molecule} dominant @subgroup {mainchain} @vectorlist {mc} color= white master= {mainchain} { n 62 } P 22.459 -3.874 52.538 { ca 62 } 21.206 -4.590 52.399 { c 62 }20.520 -4.149 51.099 { o 62 }20.512 -2.960 50.747 { c 62 }P 20.520 -4.149 51.099 { n 63 }19.939 -5.112 50.404 { ca 63 } 19.103 -4.841 49.228 { c 63 }17.717 -5.412 49.499 { o 63 }17.590 -6.583 49.871 { c 63 }P 17.717 -5.412 49.499 { n 64 }16.688 -4.594 49.317 { ca 64 } 15.337 -5.064 49.569 { c 64 }14.852 -5.880 48.406 { o 64 }15.037 -5.488 47.256 { c 64 }P 14.852 -5.880 48.406 { n 65 }14.209 -6.998 48.680 { ca 65 } 13.614 -7.751 47.604 { c 65 }12.122 -7.865 47.913 { o 65 }11.571 -7.107 48.735 { c 65 }P 12.122 -7.865 47.913 { n 66 }11.448 -8.766 47.212 { ca 66 } 10.045 -8.959 47.495 { c 66 }9.876 -9.893 48.672 { o 66 }10.227 -11.061 48.602 { c 66 }P 9.876 -9.893 48.672 { n 67 } 9.393 -9.330 49.772 { ca 67 }9.153 -10.094 50.986 { c 67 }10.439 -10.754 51.503 { o 67 }10.392 -11.823 52.107 { c 67 }P 10.439 -10.754 51.503 { n 68 } 11.587 -10.112 51.276 { ca 68 }12.873 -10.685 51.640 { c 68 }13.937 -9.640 51.364 { o 68 }13.642 -8.586 50.812 { c 68 }P 13.937 -9.640 51.364 { n 69 }15.163 -9.922 51.790 { ca 69 } 16.279 -9.006 51.572 { c 69 }17.535 -9.831 51.289 { o 69 }17.591 -11.043 51.555 { c 69 }P 17.535 -9.831 51.289 { n 70 }18.541 -9.180 50.748 { ca 70 } 19.820 -9.831 50.558 { c 70 }20.874 -8.948 51.199 { o 70 }20.794 -7.733 51.075 { c 70 }P 20.874 -8.948 51.199 { n 71 }21.898 -9.544 51.807 { ca 71 } 23.055 -8.760 52.245 { c 71 }24.247 -9.007 51.342 { o 71 }24.580 -10.151 51.046 { c 71 }P 24.247 -9.007 51.342 { n 72 }24.940 -7.940 50.980 @vectorlist {Hb} color= brown nobutton master= {mainchain} master= {Hbonds} {leu 63 hn} <1.875> P U 20.026 -6.083 50.626 {glu 70 o}U 20.564 -7.238 50.940 {asp 65 hn} <1.768> P U 14.091 -7.386 49.594 {thr 68 o}U 13.777 -8.226 50.447 {glu 70 hn} <1.966> P U 18.502 -8.229 50.441 {leu 63 o}U 17.864 -7.077 50.042 @subgroup {sidechain} @vectorlist {sc} color= cyan master= {sidechain} { atm} P 21.206 -4.590 52.399 { atm}20.294 -4.342 53.602 { atm}19.020 -5.187 53.672 { atm}19.287 -6.501 54.390 { atm} P 19.020 -5.187 53.672 { atm}17.925 -4.449 54.424 { atm} P 19.103 -4.841 49.228 { atm}19.708 -5.449 47.961 { atm}18.924 -5.231 46.665 { atm}19.866 -5.185 45.470 { atm} P 18.924 -5.231 46.665 { atm}17.930 -6.360 46.442 { atm} P 15.337 -5.064 49.569 { atm}14.394 -3.883 49.740 { atm}12.971 -4.340 50.013 { atm}12.762 -5.130 50.971 { atm} P 12.971 -4.340 50.013 { atm}12.078 -3.956 49.247 { atm} P 13.614 -7.751 47.604 { atm}14.252 -9.127 47.485 { atm}14.302 -9.625 46.051 { atm}13.300 -9.465 45.316 { atm} P 14.302 -9.625 46.051 { atm}15.348 -10.182 45.660 { atm} P 10.045 -8.959 47.495 { atm}9.277 -9.466 46.273 { atm}9.199 -8.343 45.235 { atm}8.631 -8.770 43.892 { atm} P 9.277 -9.466 46.273 { atm}7.858 -9.822 46.673 { atm} P 9.153 -10.094 50.986 { atm}8.072 -11.155 50.708 { atm}7.537 -11.765 51.966 { atm}7.458 -11.103 52.976 { atm} P 7.537 -11.765 51.966 { atm}7.148 -13.037 51.907 { atm} P 12.873 -10.685 51.640 { atm}13.184 -11.975 50.858 { atm}14.365 -12.587 51.391 { atm} P 13.184 -11.975 50.858 { atm}13.411 -11.664 49.387 { atm} P 16.279 -9.006 51.572 { atm}16.521 -8.084 52.782 { atm}15.392 -7.074 52.917 { atm} P 16.521 -8.084 52.782 { atm}16.593 -8.898 54.065 { atm} P 19.820 -9.831 50.558 { atm}20.130 -9.937 49.068 { atm}19.508 -11.131 48.385 { atm}18.062 -10.880 48.050 { atm}17.701 -9.710 47.795 { atm} P 18.062 -10.880 48.050 { atm}17.294 -11.861 48.003 { atm} P 23.055 -8.760 52.245 { atm}23.413 -9.093 53.695 { atm}22.383 -8.579 54.682 { atm}22.405 -7.409 55.065 { atm} P 22.383 -8.579 54.682 { atm}21.474 -9.455 55.094 @group {instructions} dominant @labellist {instr} color= white screen {Put labels at Tetrahedral sidechain branches} -180 180 100 @group {answer} dominant nobutton off @subgroup {} nobutton @labellist {Drawn} color= green answer { ___ leu cg} P 19.020 -5.187 53.672 { ___ leu cg} P 18.924 -5.231 46.665 { ___ ile cb} P 9.277 -9.466 46.273 { ___ thr cb} P 13.184 -11.975 50.858 { ___ val cb} P 16.521 -8.084 52.782 @kinemage 4 @caption For this next exercise: Put a ball on each Oxygen atom in the backbone of this peptide. @minutes 1.3 @drawball @bigfonts @multiwidth @zoom 1.09 @zslab 200 @center 30.859 43.193 -5.302 @matrix -0.587723 0.799995 -0.120786 0.806691 0.568010 -0.163138 -0.061902 -0.193317 -0.979182 @group {molecule} dominant @subgroup {mainchain} @vectorlist {mc} color= white { atm} <2trxH58-67 mut> P 28.826 36.221 -2.583 { atm} 28.691 37.690 -2.664 { atm}28.857 38.050 -4.145 { atm}29.933 37.847 -4.690 { atm}P 28.857 38.050 -4.145 { atm}27.733 38.539 -4.680 { atm} 27.741 38.998 -6.102 { atm}28.373 40.374 -6.128 { atm}27.835 41.349 -5.540 { atm}P 28.373 40.374 -6.128 { atm}29.501 40.517 -6.826 { atm} 30.230 41.784 -6.828 { atm}29.594 42.892 -7.703 { atm}30.062 44.009 -7.506 { atm}P 29.594 42.892 -7.703 { atm}28.660 42.559 -8.533 { atm} 27.982 43.600 -9.348 { atm}26.996 44.318 -8.413 { atm}26.880 45.548 -8.474 { atm}P 26.996 44.318 -8.413 { atm}26.348 43.477 -7.609 { atm} 25.316 44.023 -6.688 { atm}25.887 44.593 -5.422 { atm}25.228 45.439 -4.768 { atm}P 25.887 44.593 -5.422 { atm}27.059 44.181 -4.989 { atm} 27.725 44.603 -3.750 { atm}29.180 44.894 -4.070 { atm}30.044 44.018 -3.875 { atm}P 29.180 44.894 -4.070 { atm}29.452 46.060 -4.566 { atm} 30.824 46.384 -4.999 { atm}31.760 46.805 -3.907 { atm}32.952 47.008 -4.208 { atm}P 31.760 46.805 -3.907 { atm}31.322 46.971 -2.677 { atm} 32.139 47.479 -1.593 { atm}33.026 46.472 -0.910 { atm}34.080 46.911 -0.398 { atm}P 33.026 46.472 -0.910 { atm}32.689 45.181 -0.915 { atm} 33.471 44.241 -0.136 { atm}34.785 43.766 -0.811 { atm}35.771 43.733 -0.049 { atm}P 34.785 43.766 -0.811 { atm}34.711 43.426 -2.064 { atm} 35.904 42.817 -2.726 { atm}37.179 43.665 -2.537 { atm}38.247 43.146 -2.213 { atm}P 37.179 43.665 -2.537 { atm}37.050 44.959 -2.751 @subgroup {sidechain} @vectorlist {sc} color= white { atm} P 28.691 37.690 -2.664 { atm}29.665 38.408 -1.747 { atm}29.460 39.945 -1.761 { atm}29.506 40.469 -0.336 { atm}P 29.460 39.945 -1.761 { atm}30.461 40.624 -2.663 { atm} P 27.741 38.998 -6.102 { atm}26.271 38.978 -6.564 { atm}26.208 39.429 -8.032 { atm}26.661 40.532 -8.311 { atm}P 26.208 39.429 -8.032 { atm}25.700 38.534 -8.850 { atm} P 30.230 41.784 -6.828 { atm}31.732 41.539 -7.247 { atm}31.791 40.998 -8.707 { atm}33.206 41.362 -9.299 { atm}P 31.732 41.539 -7.247 { atm}32.426 40.634 -6.195 { atm} P 27.982 43.600 -9.348 { atm}27.224 43.002 -10.515 { atm}28.155 42.578 -11.643 { atm}29.275 43.023 -11.776 { atm}P 28.155 42.578 -11.643 { atm}27.652 41.731 -12.396 { atm} P 25.316 44.023 -6.688 { atm}24.305 42.932 -6.357 { atm}23.513 42.535 -7.599 { atm}22.927 41.163 -7.442 { atm}22.889 40.574 -6.367 { atm}P 22.927 41.163 -7.442 { atm}22.437 40.593 -8.558 { atm} P 27.725 44.603 -3.750 { atm}27.592 43.470 -2.724 { atm}26.143 43.165 -2.397 { atm}25.615 43.912 -1.540 { atm}P 26.143 43.165 -2.397 { atm}25.548 42.140 -2.957 { atm} P 30.824 46.384 -4.999 { atm}30.589 47.552 -5.961 { atm}29.371 48.241 -5.391 { atm}28.450 47.059 -5.018 { atm}P 29.452 46.060 -4.566 { atm}28.450 47.059 -5.018 { atm} P 33.471 44.241 -0.136 { atm}32.665 42.975 0.357 { atm}31.598 43.518 1.177 { atm}P 32.665 42.975 0.357 { atm}33.500 41.987 1.203 { atm} P 35.904 42.817 -2.726 { atm}35.633 42.615 -4.218 { atm}35.609 43.887 -5.006 { atm}36.722 44.686 -5.165 { atm}36.406 45.734 -5.903 { atm}35.131 45.645 -6.229 { atm}P 35.609 43.887 -5.006 { atm}34.609 44.500 -5.681 { atm}35.131 45.645 -6.229 @group {instructions} dominant @labellist {instructions} color= white screen {Put Balls on backbone oxygens} -180, 180, 100 @group {answer} dominant nobutton off @balllist {O balls} color= green answer { o leu 58}29.933 37.847 -4.690 { o asn 59}27.835 41.349 -5.540 { o ile 60}30.062 44.009 -7.506 { o asp 61}26.880 45.548 -8.474 { o gln 62}25.228 45.439 -4.768 { o asn 63}30.044 44.018 -3.875 { o pro 64}32.952 47.008 -4.208 { o gly 65}34.080 46.911 -0.398 { o thr 66}35.771 43.733 -0.049 { o C-term}38.247 43.146 -2.213 { o C-term}37.050 44.959 -2.751 @kinemage 5 @caption For this last exercise: Draw a line for each good H-bond in this small piece of protein. There are mainchain, sidechain-mainchain, and sidechain-sidechain H-bonds. (H atoms not shown.) @minutes 3.0 @drawline @shortline 0.7 @zoom 1.00 @zslab 200 @ztran 0 @matrix 1.000000 -0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -0.000000 1.000000 @master {mainchain} @master {sidechain} @group {molecule} dominant @subgroup {mainchain} @vectorlist {mc} color= white master= {mainchain} { n glu 2 } P 18.478 24.531 0.619 { ca glu 2 }19.240 24.741 1.886 { c glu 2 }20.671 25.200 1.614 { o glu 2 }21.343 24.641 0.763 { c glu 2 }P 20.671 25.200 1.614 { n thr 3 }21.061 26.200 2.373 { ca thr 3 }22.444 26.745 2.238 { c thr 3 }23.424 25.749 2.981 { o thr 3 }23.051 24.967 3.783 { c thr 3 }P 23.424 25.749 2.981 { n pro 4 }24.671 25.898 2.559 { ca pro 4 }25.727 25.053 3.145 { c pro 4 }25.832 25.387 4.647 { o pro 4 }26.026 24.455 5.430 { c pro 4 }P 25.832 25.387 4.647 { n ser 5 }25.675 26.612 5.036 { ca ser 5 }25.745 27.011 6.425 { c ser 5 }24.640 26.340 7.232 { o ser 5 }24.857 25.861 8.359 { c ser 5 }P 24.640 26.340 7.232 { n ala 6 }23.430 26.351 6.646 { ca ala 6 }22.267 25.744 7.297 { c ala 6 }22.430 24.247 7.390 { o ala 6 }22.041 23.630 8.398 { c ala 6 }P 22.430 24.247 7.390 { n ala 7 }22.949 23.617 6.365 { ca ala 7 }23.192 22.195 6.327 { c ala 7 }24.177 21.845 7.463 { o ala 7 }24.027 20.845 8.162 { c ala 7 }P 24.177 21.845 7.463 { n phe 8 }25.168 22.680 7.647 { ca phe 8 }26.159 22.410 8.754 { c phe 8 }25.464 22.381 10.086 { o phe 8 }25.714 21.527 10.967 { c phe 8 }P 25.464 22.381 10.086 { n leu 9 }24.602 23.358 10.360 { ca leu 9 }23.875 23.417 11.595 { c leu 9 }23.035 22.159 11.803 { o leu 9 }22.986 21.565 12.880 { c leu 9 }P 23.035 22.159 11.803 { n arg 10 }22.299 21.779 10.733 { ca arg 10 }21.453 20.602 10.796 { c arg 10 }22.214 19.305 11.033 @subgroup {sidechain} @vectorlist {sc} color= cyan master= {sidechain} { ca glu 2 }P 19.240 24.741 1.886 { cb glu 2 }19.271 23.414 2.580 { cg glu 2 }19.819 23.454 4.018 { cd glu 2 }19.847 22.078 4.598 { oe1 glu 2 }20.055 21.073 3.945 { cd glu 2 }P 19.847 22.078 4.598 { oe2 glu 2 }19.644 21.974 5.883 { ca thr 3 }P 22.444 26.745 2.238 { cb thr 3 }22.587 28.143 2.780 { og1 thr 3 }22.446 28.038 4.208 { cb thr 3 }P 22.587 28.143 2.780 { cg2 thr 3 }21.610 29.180 2.206 { ca pro 4 }P 25.727 25.053 3.145 { cb pro 4 } 26.983 25.436 2.359 { cg pro 4 }26.453 25.906 1.023 { cd pro 4 }25.199 26.673 1.406 { n pro 4 } 24.676 26.008 2.561 { ca ser 5 }P 25.745 27.011 6.425 { cb ser 5 } 25.647 28.532 6.555 { og ser 5 }25.783 28.938 7.906 { ca ala 6 }P 22.267 25.744 7.297 { cb ala 6 }20.999 26.091 6.497 { ca ala 7 }P 23.192 22.195 6.327 { cb ala 7 }23.679 21.746 4.982 { ca phe 8 }P 26.159 22.410 8.754 { cb phe 8 }27.312 23.420 8.668 { cg phe 8 }28.302 23.279 9.803 { cd1 phe 8 }29.447 22.502 9.644 { ce1 phe 8 }30.352 22.303 10.680 { cz phe 8 }30.054 22.863 11.907 { cg phe 8 }P 28.302 23.279 9.803 { cd2 phe 8 }28.070 23.866 11.044 { ce2 phe 8 }28.932 23.669 12.111 { cz phe 8 }30.054 22.863 11.907 { ca leu 9 }P 23.875 23.417 11.595 { cb leu 9 } 22.981 24.658 11.631 { cg leu 9 }23.698 26.010 11.633 { cd1 leu 9 }22.694 27.149 11.545 { cg leu 9 }P 23.698 26.010 11.633 { cd2 leu 9 }24.508 26.187 12.907 { ca arg 10 }P 21.453 20.602 10.796 { cb arg 10 }20.582 20.491 9.498 { cg arg 10 }19.641 19.279 9.461 { cd arg 10 }18.701 19.356 8.280 { ne arg 10 }19.389 19.406 7.002 { cz arg 10 }19.810 18.395 6.314 { nh1 arg 10 }19.731 17.119 6.766 { cz arg 10 }P 19.810 18.395 6.314 { nh2 arg 10 }20.426 18.535 5.177 @labellist {instr} color= white screen {Draw in all the good H-bonds} -180 180 100 @group {ref} dominant nobutton off @vectorlist {Drawn} color= green answer { o thr 3 }P 23.027 24.643 4.403 { n ala 7 }22.973 23.941 5.745 { o pro 4 }P 25.824 24.036 5.953 { n phe 8 }25.370 23.099 7.124 { o ser 5 }P 24.801 25.316 8.795 { n leu 9 }24.658 23.903 9.924 { o ala 6 }P 22.101 23.197 8.945 { n arg 10 }22.239 22.212 10.186 { og1 thr 3 }P 22.667 27.660 4.754 { n ala 6 }23.209 26.729 6.100 { oe2 glu 2 }P 19.581 21.335 6.161 { ne arg 10 }19.452 20.045 6.724 { oe1 glu 2 }P 20.146 20.449 4.248 { nh2 arg 10 }20.335 19.159 4.874