[Chimera-users] H-bonds - molecules selection questions
Tom Goddard
goddard at sonic.net
Thu Oct 18 17:20:00 PDT 2012
Hi Marek,
There is a Chimera keyboard shortcut "sc" that extends a selection of
atoms to all connected atoms. You can enable keyboard shortcuts with
menu Tools / General Controls / Keyboard Shortcuts and click the Enable
button in the shortcuts dialog. This setting will be remembered in
subsequent sessions. Then just typing sc will extend the current
selection. Another way to use the shortcut without turning them on is
the command "ac sc". This says run the shortcut "sc". The "ac" command
stands for accelerators, another word for shortcut. You can also enable
keyboard shortcuts using the Chimera command "ac" with no arguments.
And the keyboard shortcut "cl" (standards for command-line) allows you
to go back to typing commands instead of shortcuts.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html
Tom
-------- Original Message --------
Subject: Re: [Chimera-users] H-bonds - molecules selection questions
From: Marek Maly
To: chimera-users at cgl.ucsf.edu
Date: 10/18/12 4:57 PM
> Hi Eric,
>
> thanks for your prompt comments !
>
> Unfortunately your advices did not help in points #1,#2 (#3 is working
> perfectly, I see here
> some inspiration from C++ destructor labeling :)) ).
>
> The problem is perhaps in what you pointed out i.e.
>
> necessity of implementation of this hierarchy:
>
> atom -> residue -> connected fragment (molecule) -> model
>
> For the case you would be so kind and try in the future to implement this
> alternative level of objects manipulation (hierarchy) in Chimera, below I
> pasted small testing system for you. There are just two fragments of
> some polymer molecule (one composed of G1X and second composed of REP
> residues)
> and few molecules of water.
>
> The polymers are bonded via 1 hydrogen bond. The water molecules was
> selected
> as the close shell of the G1X based molecule so there are some more
> HBs mainly
> between WAT and G1X. There is moreover also 1 intramolecular bond in
> REP based molecule.
>
> Just two more related suggestions:
>
> A)
> Regarding H-bonds, it would be nice to have the possibility to
> set condition (e.g. in H-bond menu panel ).
>
> "Show only INTERMOLECULAR H-bonds".
>
> Imagine for example system of several sugar molecules in water, where
> I would like to visualize only H-bonds between different sugar molecules,
> and not the plethora of intramolecular H-bonds within individual sugar
> molecules.
>
> B)
> Would be also nice to have the possibility to select molecule (or more
> generally any compact (by connectivity) fragment) by mouse (not only by
> Favorites -> Model panel -> Select chain (especially if the list of
> chains is too long
> to fit into this menu)).
>
> For example in Materials Studio from Accelrys one can select one
> atom on the given fragment and then using right-mouse-button-menu he
> can perform selection of the whole (by connectivity) fragment by one
> click.
>
>
> I believe that introducing/extension of the molecular or more
> generally "by connection fragment" manipulation possibilities in
> Chimera will be very useful and appreciated feature, especially for
> those of us working with some heterogenous/hybrid systems (not only
> proteins) and using different input formats e.g. Amber files where the
> concept of chain as the "some molecular representant" many times might
> have problems simply because the chain identification record is
> missing. On the other hand the connectivity condition is pretty
> general and based on it one can do the system fragmentation
> independently on it's composition or on the input format.
>
> Thank you very much in advance !
>
> Best wishes,
>
> Marek
>
> TESTING SYSTEM
>
> ATOM 1 C22 G1X 212 96.455 43.267 88.908 1.00
> 0.00 C
> ATOM 2 H44 G1X 212 96.026 43.977 89.619 1.00
> 0.00 H
> ATOM 3 O4 G1X 212 97.536 43.939 88.355 1.00
> 0.00 O
> ATOM 4 C21 G1X 213 97.071 45.034 87.548 1.00
> 0.00 C
> ATOM 5 H42 G1X 213 96.711 44.689 86.576 1.00
> 0.00 H
> ATOM 6 H41 G1X 213 96.320 45.662 88.033 1.00
> 0.00 H
> ATOM 7 C22 G1X 213 98.390 45.878 87.325 1.00
> 0.00 C
> ATOM 8 H44 G1X 213 98.373 46.620 86.522 1.00
> 0.00 H
> ATOM 9 H43 G1X 213 99.214 45.179 87.162 1.00
> 0.00 H
> ATOM 10 O4 G1X 213 98.678 46.666 88.498 1.00
> 0.00 O
> ATOM 11 C21 G1X 214 99.631 47.790 88.315 1.00
> 0.00 C
> ATOM 12 H42 G1X 214 100.116 47.602 87.354 1.00
> 0.00 H
> ATOM 13 H41 G1X 214 99.047 48.702 88.171 1.00
> 0.00 H
> ATOM 14 C22 G1X 214 100.654 47.965 89.540 1.00
> 0.00 C
> ATOM 15 H44 G1X 214 101.617 48.273 89.125 1.00
> 0.00 H
> ATOM 16 H43 G1X 214 100.870 46.987 89.978 1.00
> 0.00 H
> ATOM 17 O4 G1X 214 100.194 48.975 90.451 1.00
> 0.00 O
> ATOM 18 C21 G1X 215 98.968 48.734 91.173 1.00
> 0.00 C
> ATOM 19 H42 G1X 215 98.095 49.067 90.607 1.00
> 0.00 H
> ATOM 20 H41 G1X 215 98.850 47.664 91.365 1.00
> 0.00 H
> ATOM 21 C22 G1X 215 98.942 49.441 92.544 1.00
> 0.00 C
> ATOM 22 H44 G1X 215 99.762 48.979 93.100 1.00
> 0.00 H
> ATOM 23 H43 G1X 215 97.967 49.294 93.015 1.00
> 0.00 H
> ATOM 24 O4 G1X 215 98.955 50.883 92.495 1.00
> 0.00 O
> ATOM 25 C21 G1X 216 98.795 51.619 93.801 1.00
> 0.00 C
> ATOM 26 H42 G1X 216 98.122 51.160 94.530 1.00
> 0.00 H
> ATOM 27 H41 G1X 216 99.774 51.885 94.208 1.00
> 0.00 H
> ATOM 28 C22 G1X 216 98.200 53.013 93.518 1.00
> 0.00 C
> ATOM 29 H44 G1X 216 98.795 53.483 92.731 1.00
> 0.00 H
> ATOM 30 H43 G1X 216 98.154 53.659 94.398 1.00
> 0.00 H
> ATOM 31 O4 G1X 216 96.776 52.720 93.291 1.00
> 0.00 O
> ATOM 32 C21 G1X 217 96.189 53.859 92.565 1.00
> 0.00 C
> ATOM 33 H42 G1X 217 96.437 54.746 93.153 1.00
> 0.00 H
> ATOM 34 H41 G1X 217 96.582 53.879 91.545 1.00
> 0.00 H
> ATOM 35 C22 G1X 217 94.719 53.584 92.462 1.00
> 0.00 C
> ATOM 36 H44 G1X 217 94.530 52.708 91.836 1.00
> 0.00 H
> ATOM 37 H43 G1X 217 94.180 54.385 91.948 1.00
> 0.00 H
> ATOM 38 O4 G1X 217 94.070 53.449 93.774 1.00
> 0.00 O
> ATOM 39 C21 G1X 218 94.246 54.573 94.721 1.00
> 0.00 C
> ATOM 40 H42 G1X 218 95.228 54.695 95.187 1.00
> 0.00 H
> ATOM 41 H41 G1X 218 93.969 55.508 94.229 1.00
> 0.00 H
> ATOM 42 C22 G1X 218 93.271 54.281 95.804 1.00
> 0.00 C
> ATOM 43 H44 G1X 218 92.271 54.034 95.440 1.00
> 0.00 H
> ATOM 44 H43 G1X 218 93.183 55.150 96.460 1.00
> 0.00 H
> ATOM 45 O4 G1X 218 93.723 53.293 96.711 1.00
> 0.00 O
> ATOM 46 C21 G1X 219 92.717 52.989 97.735 1.00
> 0.00 C
> ATOM 47 H42 G1X 219 93.035 53.489 98.654 1.00
> 0.00 H
> ATOM 48 H41 G1X 219 91.728 53.390 97.501 1.00
> 0.00 H
> ATOM 49 C22 G1X 219 92.652 51.524 97.972 1.00
> 0.00 C
> ATOM 50 H44 G1X 219 92.649 51.001 97.012 1.00
> 0.00 H
> ATOM 51 H43 G1X 219 91.771 51.271 98.567 1.00
> 0.00 H
> ATOM 52 O4 G1X 219 93.726 51.012 98.744 1.00
> 0.00 O
> ATOM 53 C21 G1X 220 93.771 49.605 98.985 1.00
> 0.00 C
> ATOM 54 H42 G1X 220 93.016 49.392 99.746 1.00
> 0.00 H
> ATOM 55 H41 G1X 220 93.506 49.101 98.052 1.00
> 0.00 H
> ATOM 56 C22 G1X 220 95.138 49.082 99.489 1.00
> 0.00 C
> ATOM 57 H44 G1X 220 95.278 47.998 99.503 1.00
> 0.00 H
> ATOM 58 H43 G1X 220 95.229 49.493 100.497 1.00
> 0.00 H
> ATOM 59 O4 G1X 220 96.229 49.613 98.727 1.00
> 0.00 O
> ATOM 60 C21 G1X 221 97.197 48.654 98.364 1.00
> 0.00 C
> ATOM 61 H42 G1X 221 96.617 47.751 98.155 1.00
> 0.00 H
> ATOM 62 H41 G1X 221 97.726 48.984 97.467 1.00
> 0.00 H
> ATOM 63 C22 G1X 221 98.158 48.374 99.444 1.00
> 0.00 C
> ATOM 64 H44 G1X 221 98.394 49.268 100.027 1.00
> 0.00 H
> ATOM 65 H43 G1X 221 99.064 47.932 99.021 1.00
> 0.00 H
> ATOM 66 O4 G1X 221 97.612 47.364 100.355 1.00
> 0.00 O
> ATOM 67 C21 G1X 222 98.390 47.136 101.549 1.00
> 0.00 C
> ATOM 68 H42 G1X 222 99.229 46.503 101.247 1.00
> 0.00 H
> ATOM 69 H41 G1X 222 98.685 48.082 102.010 1.00
> 0.00 H
> ATOM 70 C22 G1X 222 97.433 46.406 102.553 1.00
> 0.00 C
> ATOM 71 H44 G1X 222 98.019 45.999 103.381 1.00
> 0.00 H
> ATOM 72 H43 G1X 222 96.770 45.646 102.133 1.00
> 0.00 H
> ATOM 73 O4 G1X 222 96.551 47.389 103.125 1.00
> 0.00 O
> ATOM 74 C21 G1X 223 95.534 46.829 104.014 1.00
> 0.00 C
> ATOM 75 H42 G1X 223 94.642 46.540 103.452 1.00
> 0.00 H
> ATOM 76 H41 G1X 223 95.994 46.034 104.607 1.00
> 0.00 H
> ATOM 77 C22 G1X 223 95.225 47.970 104.956 1.00
> 0.00 C
> ATOM 78 H44 G1X 223 94.382 47.653 105.574 1.00
> 0.00 H
> ATOM 79 H43 G1X 223 95.001 48.877 104.387 1.00
> 0.00 H
> ATOM 80 O4 G1X 223 96.407 48.266 105.748 1.00
> 0.00 O
> ATOM 81 C21 G1X 224 96.538 47.399 106.941 1.00
> 0.00 C
> ATOM 82 H42 G1X 224 95.619 47.433 107.532 1.00
> 0.00 H
> ATOM 83 H41 G1X 224 96.881 46.402 106.650 1.00
> 0.00 H
> ATOM 84 C22 G1X 224 97.659 47.928 107.912 1.00
> 0.00 C
> ATOM 85 H44 G1X 224 97.636 47.431 108.885 1.00
> 0.00 H
> ATOM 86 H43 G1X 224 97.546 49.008 108.036 1.00
> 0.00 H
> ATOM 87 O4 G1X 224 99.000 47.725 107.400 1.00
> 0.00 O
> ATOM 88 C21 G1X 225 100.047 48.553 107.969 1.00
> 0.00 C
> ATOM 89 H42 G1X 225 99.716 49.594 107.925 1.00
> 0.00 H
> ATOM 90 H41 G1X 225 100.281 48.252 108.993 1.00
> 0.00 H
> ATOM 91 C22 G1X 225 101.389 48.242 107.158 1.00
> 0.00 C
> ATOM 92 H44 G1X 225 101.674 47.207 107.360 1.00
> 0.00 H
> ATOM 93 H43 G1X 225 102.123 48.980 107.493 1.00
> 0.00 H
> ATOM 94 O4 G1X 225 101.171 48.422 105.756 1.00
> 0.00 O
> TER
> ATOM 95 O4 REP 418 90.187 52.468 109.473 1.00
> 0.00 O
> ATOM 96 C4 REP 418 89.201 51.367 109.355 1.00
> 0.00 C
> ATOM 97 H4 REP 418 88.305 51.742 109.850 1.00
> 0.00 H
> ATOM 98 C3 REP 418 88.861 50.953 107.901 1.00
> 0.00 C
> ATOM 99 O3 REP 418 88.013 52.032 107.389 1.00
> 0.00 O
> ATOM 100 H3O REP 418 88.333 52.934 107.460 1.00
> 0.00 H
> ATOM 101 H3 REP 418 89.821 50.783 107.414 1.00
> 0.00 H
> ATOM 102 C2 REP 418 88.047 49.733 107.692 1.00
> 0.00 C
> ATOM 103 H2 REP 418 87.072 49.975 108.129 1.00
> 0.00 H
> ATOM 104 N2 REP 418 87.736 49.292 106.270 1.00
> 0.00 N
> ATOM 105 H21 REP 418 87.087 48.514 106.069 1.00
> 0.00 H
> ATOM 106 H23 REP 418 88.560 48.924 105.768 1.00
> 0.00 H
> ATOM 107 H22 REP 418 87.378 50.018 105.628 1.00
> 0.00 H
> ATOM 108 C5 REP 418 89.719 50.109 110.108 1.00
> 0.00 C
> ATOM 109 H5 REP 418 90.693 49.789 109.738 1.00
> 0.00 H
> ATOM 110 C6 REP 418 89.977 50.283 111.559 1.00
> 0.00 C
> ATOM 111 H61 REP 418 89.103 50.788 111.970 1.00
> 0.00 H
> ATOM 112 O6 REP 418 90.066 48.997 112.228 1.00
> 0.00 O
> ATOM 113 H6O REP 418 89.199 48.589 112.272 1.00
> 0.00 H
> ATOM 114 H62 REP 418 90.881 50.843 111.801 1.00
> 0.00 H
> ATOM 115 O5 REP 418 88.633 49.096 109.940 1.00
> 0.00 O
> ATOM 116 C1 REP 418 88.589 48.607 108.563 1.00
> 0.00 C
> ATOM 117 H1 REP 418 89.543 48.276 108.153 1.00
> 0.00 H
> ATOM 118 O4 REP 419 95.465 51.939 107.147 1.00
> 0.00 O
> ATOM 119 C4 REP 419 94.270 52.162 108.007 1.00
> 0.00 C
> ATOM 120 H4 REP 419 94.578 51.970 109.035 1.00
> 0.00 H
> ATOM 121 C3 REP 419 93.609 53.509 107.855 1.00
> 0.00 C
> ATOM 122 O3 REP 419 94.541 54.518 108.330 1.00
> 0.00 O
> ATOM 123 H3O REP 419 95.447 54.362 108.052 1.00
> 0.00 H
> ATOM 124 H3 REP 419 93.367 53.773 106.826 1.00
> 0.00 H
> ATOM 125 C2 REP 419 92.278 53.610 108.783 1.00
> 0.00 C
> ATOM 126 H2 REP 419 92.518 53.482 109.844 1.00
> 0.00 H
> ATOM 127 N2 REP 419 91.635 55.003 108.738 1.00
> 0.00 N
> ATOM 128 H21 REP 419 92.258 55.794 108.970 1.00
> 0.00 H
> ATOM 129 H23 REP 419 90.778 55.052 109.312 1.00
> 0.00 H
> ATOM 130 H22 REP 419 91.272 55.186 107.788 1.00
> 0.00 H
> ATOM 131 C5 REP 419 93.267 50.994 107.634 1.00
> 0.00 C
> ATOM 132 H5 REP 419 92.995 51.169 106.593 1.00
> 0.00 H
> ATOM 133 C6 REP 419 93.794 49.586 107.829 1.00
> 0.00 C
> ATOM 134 H61 REP 419 94.240 49.486 108.819 1.00
> 0.00 H
> ATOM 135 O6 REP 419 92.733 48.640 107.607 1.00
> 0.00 O
> ATOM 136 H6O REP 419 92.320 48.925 106.788 1.00
> 0.00 H
> ATOM 137 H62 REP 419 94.577 49.347 107.109 1.00
> 0.00 H
> ATOM 138 O5 REP 419 92.065 51.199 108.510 1.00
> 0.00 O
> ATOM 139 C1 REP 419 91.343 52.494 108.451 1.00
> 0.00 C
> ATOM 140 H1 REP 419 90.811 52.655 107.513 1.00
> 0.00 H
> ATOM 141 O4 REP 420 95.590 52.180 101.312 1.00
> 0.00 O
> ATOM 142 C4 REP 420 95.652 51.657 102.735 1.00
> 0.00 C
> ATOM 143 H4 REP 420 95.847 50.585 102.710 1.00
> 0.00 H
> ATOM 144 C3 REP 420 96.846 52.212 103.561 1.00
> 0.00 C
> ATOM 145 O3 REP 420 98.135 51.913 103.083 1.00
> 0.00 O
> ATOM 146 H3O REP 420 98.285 50.981 103.257 1.00
> 0.00 H
> ATOM 147 H3 REP 420 96.838 53.302 103.594 1.00
> 0.00 H
> ATOM 148 C2 REP 420 96.757 51.844 105.049 1.00
> 0.00 C
> ATOM 149 H2 REP 420 96.742 50.768 105.254 1.00
> 0.00 H
> ATOM 150 N2 REP 420 97.949 52.458 105.775 1.00
> 0.00 N
> ATOM 151 H21 REP 420 97.931 52.107 106.746 1.00
> 0.00 H
> ATOM 152 H23 REP 420 97.831 53.478 105.885 1.00
> 0.00 H
> ATOM 153 H22 REP 420 98.884 52.198 105.421 1.00
> 0.00 H
> ATOM 154 C5 REP 420 94.283 51.937 103.400 1.00
> 0.00 C
> ATOM 155 H5 REP 420 94.038 52.998 103.353 1.00
> 0.00 H
> ATOM 156 C6 REP 420 93.079 51.261 102.728 1.00
> 0.00 C
> ATOM 157 H61 REP 420 93.124 51.476 101.660 1.00
> 0.00 H
> ATOM 158 O6 REP 420 93.091 49.803 103.103 1.00
> 0.00 O
> ATOM 159 H6O REP 420 92.499 49.622 103.837 1.00
> 0.00 H
> ATOM 160 H62 REP 420 92.115 51.623 103.084 1.00
> 0.00 H
> ATOM 161 O5 REP 420 94.472 51.711 104.837 1.00
> 0.00 O
> ATOM 162 C1 REP 420 95.460 52.405 105.702 1.00
> 0.00 C
> ATOM 163 H1 REP 420 95.580 53.484 105.605 1.00
> 0.00 H
> ATOM 164 O4 REP 421 97.348 57.362 99.522 1.00
> 0.00 O
> ATOM 165 C4 REP 421 96.503 56.121 99.834 1.00
> 0.00 C
> ATOM 166 H4 REP 421 95.525 56.591 99.737 1.00
> 0.00 H
> ATOM 167 C3 REP 421 96.663 54.860 98.943 1.00
> 0.00 C
> ATOM 168 O3 REP 421 96.193 55.145 97.605 1.00
> 0.00 O
> ATOM 169 H3O REP 421 96.635 55.926 97.263 1.00
> 0.00 H
> ATOM 170 H3 REP 421 97.726 54.616 98.950 1.00
> 0.00 H
> ATOM 171 C2 REP 421 95.920 53.655 99.479 1.00
> 0.00 C
> ATOM 172 H2 REP 421 94.852 53.856 99.341 1.00
> 0.00 H
> ATOM 173 N2 REP 421 96.122 52.478 98.558 1.00
> 0.00 N
> ATOM 174 H21 REP 421 95.556 51.645 98.789 1.00
> 0.00 H
> ATOM 175 H23 REP 421 97.056 52.039 98.595 1.00
> 0.00 H
> ATOM 176 H22 REP 421 95.939 52.712 97.569 1.00
> 0.00 H
> ATOM 177 C5 REP 421 96.640 55.762 101.318 1.00
> 0.00 C
> ATOM 178 H5 REP 421 97.650 55.460 101.593 1.00
> 0.00 H
> ATOM 179 C6 REP 421 96.314 56.904 102.368 1.00
> 0.00 C
> ATOM 180 H61 REP 421 97.081 57.651 102.162 1.00
> 0.00 H
> ATOM 181 O6 REP 421 95.004 57.500 102.028 1.00
> 0.00 O
> ATOM 182 H6O REP 421 94.377 57.225 102.702 1.00
> 0.00 H
> ATOM 183 H62 REP 421 96.305 56.631 103.423 1.00
> 0.00 H
> ATOM 184 O5 REP 421 95.813 54.568 101.660 1.00
> 0.00 O
> ATOM 185 C1 REP 421 96.280 53.421 100.943 1.00
> 0.00 C
> ATOM 186 H1 REP 421 97.349 53.229 101.045 1.00
> 0.00 H
> ATOM 187 O4 REP 422 102.934 58.246 99.155 1.00
> 0.00 O
> ATOM 188 C4 REP 422 101.545 58.020 99.738 1.00
> 0.00 C
> ATOM 189 H4 REP 422 101.605 58.316 100.786 1.00
> 0.00 H
> ATOM 190 C3 REP 422 100.595 58.918 98.866 1.00
> 0.00 C
> ATOM 191 O3 REP 422 100.930 60.312 98.984 1.00
> 0.00 O
> ATOM 192 H3O REP 422 101.817 60.347 99.349 1.00
> 0.00 H
> ATOM 193 H3 REP 422 100.799 58.738 97.811 1.00
> 0.00 H
> ATOM 194 C2 REP 422 99.117 58.832 99.218 1.00
> 0.00 C
> ATOM 195 H2 REP 422 98.964 59.127 100.262 1.00
> 0.00 H
> ATOM 196 N2 REP 422 98.264 59.768 98.384 1.00
> 0.00 N
> ATOM 197 H21 REP 422 97.241 59.807 98.522 1.00
> 0.00 H
> ATOM 198 H23 REP 422 98.376 59.588 97.373 1.00
> 0.00 H
> ATOM 199 H22 REP 422 98.472 60.780 98.408 1.00
> 0.00 H
> ATOM 200 C5 REP 422 101.050 56.608 99.646 1.00
> 0.00 C
> ATOM 201 H5 REP 422 101.277 56.179 98.670 1.00
> 0.00 H
> ATOM 202 C6 REP 422 101.814 55.657 100.604 1.00
> 0.00 C
> ATOM 203 H61 REP 422 101.502 55.807 101.637 1.00
> 0.00 H
> ATOM 204 O6 REP 422 101.674 54.328 100.210 1.00
> 0.00 O
> ATOM 205 H6O REP 422 100.982 53.934 100.746 1.00
> 0.00 H
> ATOM 206 H62 REP 422 102.872 55.918 100.569 1.00
> 0.00 H
> ATOM 207 O5 REP 422 99.625 56.559 99.872 1.00
> 0.00 O
> ATOM 208 C1 REP 422 98.747 57.350 98.992 1.00
> 0.00 C
> ATOM 209 H1 REP 422 98.796 56.939 97.984 1.00
> 0.00 H
> ATOM 210 O4 REP 423 106.469 62.129 101.182 1.00
> 0.00 O
> ATOM 211 C4 REP 423 105.567 61.501 100.210 1.00
> 0.00 C
> ATOM 212 H4 REP 423 105.551 62.086 99.290 1.00
> 0.00 H
> ATOM 213 C3 REP 423 106.112 60.052 99.827 1.00
> 0.00 C
> ATOM 214 O3 REP 423 107.210 60.208 98.980 1.00
> 0.00 O
> ATOM 215 H3O REP 423 107.711 61.010 99.145 1.00
> 0.00 H
> ATOM 216 H3 REP 423 106.441 59.601 100.764 1.00
> 0.00 H
> ATOM 217 C2 REP 423 105.072 59.246 99.077 1.00
> 0.00 C
> ATOM 218 H2 REP 423 104.672 59.868 98.270 1.00
> 0.00 H
> ATOM 219 N2 REP 423 105.611 57.936 98.337 1.00
> 0.00 N
> ATOM 220 H21 REP 423 106.233 58.235 97.568 1.00
> 0.00 H
> ATOM 221 H23 REP 423 104.855 57.345 97.953 1.00
> 0.00 H
> ATOM 222 H22 REP 423 106.020 57.262 99.004 1.00
> 0.00 H
> ATOM 223 C5 REP 423 104.259 61.356 101.023 1.00
> 0.00 C
> ATOM 224 H5 REP 423 104.428 61.025 102.048 1.00
> 0.00 H
> ATOM 225 C6 REP 423 103.566 62.760 100.964 1.00
> 0.00 C
> ATOM 226 H61 REP 423 103.233 62.807 99.927 1.00
> 0.00 H
> ATOM 227 O6 REP 423 102.515 62.785 101.867 1.00
> 0.00 O
> ATOM 228 H6O REP 423 101.950 63.504 101.577 1.00
> 0.00 H
> ATOM 229 H62 REP 423 104.231 63.590 101.202 1.00
> 0.00 H
> ATOM 230 O5 REP 423 103.380 60.377 100.233 1.00
> 0.00 O
> ATOM 231 C1 REP 423 103.924 59.018 100.003 1.00
> 0.00 C
> ATOM 232 H1 REP 423 104.328 58.496 100.870 1.00
> 0.00 H
> TER
> ATOM 233 O WAT 8272 89.632 50.947 97.120 1.00
> 0.00 O
> ATOM 234 H1 WAT 8272 90.089 50.746 96.304 1.00
> 0.00 H
> ATOM 235 H2 WAT 8272 90.018 50.354 97.764 1.00
> 0.00 H
> TER
> ATOM 251 O WAT 11496 92.862 54.987 89.972 1.00
> 0.00 O
> ATOM 252 H1 WAT 11496 92.091 55.549 90.043 1.00
> 0.00 H
> ATOM 253 H2 WAT 11496 92.533 54.178 89.578 1.00
> 0.00 H
> TER
> ATOM 260 O WAT 12716 98.254 43.043 105.536 1.00
> 0.00 O
> ATOM 261 H1 WAT 12716 98.423 43.984 105.494 1.00
> 0.00 H
> ATOM 262 H2 WAT 12716 97.465 42.965 106.073 1.00
> 0.00 H
> TER
> ATOM 287 O WAT 17791 98.108 51.562 90.063 1.00
> 0.00 O
> ATOM 288 H1 WAT 17791 98.380 52.477 90.137 1.00
> 0.00 H
> ATOM 289 H2 WAT 17791 98.419 51.152 90.870 1.00
> 0.00 H
> TER
> ATOM 290 O WAT 19717 99.044 45.772 94.230 1.00
> 0.00 O
> ATOM 291 H1 WAT 19717 99.024 45.771 93.273 1.00
> 0.00 H
> ATOM 292 H2 WAT 19717 98.248 46.239 94.485 1.00
> 0.00 H
> TER
> ATOM 296 O WAT 22258 99.822 48.158 84.678 1.00
> 0.00 O
> ATOM 297 H1 WAT 22258 98.887 47.969 84.758 1.00
> 0.00 H
> ATOM 298 H2 WAT 22258 100.254 47.387 85.045 1.00
> 0.00 H
> TER
> ATOM 299 O WAT 22297 94.598 47.795 89.226 1.00
> 0.00 O
> ATOM 300 H1 WAT 22297 95.121 48.549 89.498 1.00
> 0.00 H
> ATOM 301 H2 WAT 22297 93.730 47.961 89.594 1.00
> 0.00 H
> TER
> ATOM 305 O WAT 22693 93.752 50.295 91.548 1.00
> 0.00 O
> ATOM 306 H1 WAT 22693 94.578 50.691 91.269 1.00
> 0.00 H
> ATOM 307 H2 WAT 22693 93.393 49.903 90.752 1.00
> 0.00 H
> TER
> ATOM 308 O WAT 22960 101.852 45.813 100.474 1.00
> 0.00 O
> ATOM 309 H1 WAT 22960 102.475 45.425 101.088 1.00
> 0.00 H
> ATOM 310 H2 WAT 22960 101.058 45.288 100.575 1.00
> 0.00 H
> TER
> ATOM 311 O WAT 23035 100.879 45.703 84.901 1.00
> 0.00 O
> ATOM 312 H1 WAT 23035 101.173 44.812 84.709 1.00
> 0.00 H
> ATOM 313 H2 WAT 23035 101.420 45.978 85.642 1.00
> 0.00 H
> TER
> ATOM 317 O WAT 24736 95.945 50.138 89.045 1.00
> 0.00 O
> ATOM 318 H1 WAT 24736 96.674 50.709 89.290 1.00
> 0.00 H
> ATOM 319 H2 WAT 24736 95.700 50.426 88.166 1.00
> 0.00 H
> TER
> ATOM 326 O WAT 25130 104.726 46.609 107.606 1.00
> 0.00 O
> ATOM 327 H1 WAT 25130 103.987 46.033 107.410 1.00
> 0.00 H
> ATOM 328 H2 WAT 25130 105.155 46.200 108.357 1.00
> 0.00 H
> TER
> ATOM 335 O WAT 27759 95.795 42.582 103.232 1.00
> 0.00 O
> ATOM 336 H1 WAT 27759 95.348 43.037 103.946 1.00
> 0.00 H
> ATOM 337 H2 WAT 27759 95.761 43.196 102.499 1.00
> 0.00 H
> TER
> ATOM 338 O WAT 27818 91.139 50.320 94.998 1.00
> 0.00 O
> ATOM 339 H1 WAT 27818 91.223 51.053 94.388 1.00
> 0.00 H
> ATOM 340 H2 WAT 27818 91.691 49.633 94.625 1.00
> 0.00 H
> TER
> ATOM 350 O WAT 29261 100.320 51.262 105.438 1.00
> 0.00 O
> ATOM 351 H1 WAT 29261 101.016 51.347 106.090 1.00
> 0.00 H
> ATOM 352 H2 WAT 29261 100.559 50.486 104.932 1.00
> 0.00 H
> TER
> ATOM 356 O WAT 29722 98.439 44.943 91.407 1.00
> 0.00 O
> ATOM 357 H1 WAT 29722 99.112 44.369 91.774 1.00
> 0.00 H
> ATOM 358 H2 WAT 29722 98.840 45.309 90.619 1.00
> 0.00 H
> TER
> ATOM 362 O WAT 30094 92.229 57.282 93.446 1.00
> 0.00 O
> ATOM 363 H1 WAT 30094 92.342 58.143 93.850 1.00
> 0.00 H
> ATOM 364 H2 WAT 30094 92.569 57.388 92.558 1.00
> 0.00 H
> TER
> ATOM 371 O WAT 31397 91.524 51.587 92.694 1.00
> 0.00 O
> ATOM 372 H1 WAT 31397 92.168 52.271 92.878 1.00
> 0.00 H
> ATOM 373 H2 WAT 31397 92.030 50.887 92.282 1.00
> 0.00 H
> TER
> ATOM 374 O WAT 31544 98.294 49.265 104.119 1.00
> 0.00 O
> ATOM 375 H1 WAT 31544 97.486 48.751 104.116 1.00
> 0.00 H
> ATOM 376 H2 WAT 31544 98.848 48.837 104.772 1.00
> 0.00 H
> TER
> ATOM 382 O WAT 32541 90.619 54.963 93.190 1.00
> 0.00 O
> ATOM 383 H1 WAT 32541 90.995 55.831 93.339 1.00
> 0.00 H
> ATOM 384 H2 WAT 32541 91.377 54.380 93.138 1.00
> 0.00 H
> TER
> ATOM 388 O WAT 33454 95.866 45.874 91.405 1.00
> 0.00 O
> ATOM 389 H1 WAT 33454 96.725 45.480 91.553 1.00
> 0.00 H
> ATOM 390 H2 WAT 33454 95.901 46.194 90.504 1.00
> 0.00 H
> TER
> ATOM 394 O WAT 33652 99.700 45.449 105.307 1.00
> 0.00 O
> ATOM 395 H1 WAT 33652 99.834 46.392 105.400 1.00
> 0.00 H
> ATOM 396 H2 WAT 33652 100.166 45.220 104.502 1.00
> 0.00 H
> TER
> ATOM 397 O WAT 33922 99.275 55.142 95.843 1.00
> 0.00 O
> ATOM 398 H1 WAT 33922 98.529 55.726 95.984 1.00
> 0.00 H
> ATOM 399 H2 WAT 33922 99.029 54.329 96.283 1.00
> 0.00 H
> TER
> ATOM 400 O WAT 34289 90.630 48.323 98.831 1.00
> 0.00 O
> ATOM 401 H1 WAT 34289 90.829 48.040 97.939 1.00
> 0.00 H
> ATOM 402 H2 WAT 34289 89.801 48.795 98.754 1.00
> 0.00 H
> TER
> ATOM 403 O WAT 34536 94.236 45.069 86.079 1.00
> 0.00 O
> ATOM 404 H1 WAT 34536 94.565 45.077 85.180 1.00
> 0.00 H
> ATOM 405 H2 WAT 34536 94.260 45.987 86.350 1.00
> 0.00 H
> TER
> ATOM 406 O WAT 34640 102.182 53.240 93.757 1.00
> 0.00 O
> ATOM 407 H1 WAT 34640 102.770 53.433 93.027 1.00
> 0.00 H
> ATOM 408 H2 WAT 34640 101.644 52.512 93.446 1.00
> 0.00 H
> TER
> ATOM 409 O WAT 35038 102.972 44.422 107.132 1.00
> 0.00 O
> ATOM 410 H1 WAT 35038 102.998 43.687 106.519 1.00
> 0.00 H
> ATOM 411 H2 WAT 35038 102.139 44.321 107.592 1.00
> 0.00 H
> TER
> ATOM 412 O WAT 35409 94.710 48.124 86.446 1.00
> 0.00 O
> ATOM 413 H1 WAT 35409 94.744 47.984 87.392 1.00
> 0.00 H
> ATOM 414 H2 WAT 35409 94.234 48.948 86.342 1.00
> 0.00 H
> TER
> ATOM 415 O WAT 35602 100.932 50.178 100.740 1.00
> 0.00 O
> ATOM 416 H1 WAT 35602 101.380 50.165 101.586 1.00
> 0.00 H
> ATOM 417 H2 WAT 35602 101.319 49.450 100.253 1.00
> 0.00 H
> TER
> ATOM 421 O WAT 36073 100.771 52.490 91.123 1.00
> 0.00 O
> ATOM 422 H1 WAT 36073 100.295 51.697 91.371 1.00
> 0.00 H
> ATOM 423 H2 WAT 36073 101.693 52.258 91.229 1.00
> 0.00 H
> TER
> ATOM 427 O WAT 36701 95.893 51.949 95.816 1.00
> 0.00 O
> ATOM 428 H1 WAT 36701 94.983 52.236 95.887 1.00
> 0.00 H
> ATOM 429 H2 WAT 36701 96.145 52.173 94.920 1.00
> 0.00 H
> TER
> ATOM 430 O WAT 37062 100.410 44.195 107.724 1.00
> 0.00 O
> ATOM 431 H1 WAT 37062 100.458 44.743 106.941 1.00
> 0.00 H
> ATOM 432 H2 WAT 37062 100.050 43.364 107.412 1.00
> 0.00 H
> TER
> ATOM 433 O WAT 37407 98.986 45.537 110.050 1.00
> 0.00 O
> ATOM 434 H1 WAT 37407 99.364 44.989 109.362 1.00
> 0.00 H
> ATOM 435 H2 WAT 37407 98.042 45.401 109.974 1.00
> 0.00 H
>
>
>
> Dne Wed, 17 Oct 2012 23:50:31 +0200 Eric Pettersen <pett at cgl.ucsf.edu>
> napsal/-a:
>
>> On Oct 17, 2012, at 9:47 AM, Marek Maly wrote:
>>
>>> Hello all,
>>>
>>> #1
>>> I am just curious if it is in Chimera implemented possibility
>>> to select all the molecules which are connected via H-bonds with
>>> previously
>>> selected ("primary") molecule.
>>>
>>> If it is not implemented I would vote for putting it in the
>>> developers queue
>>> as it would allow to show easily and clearly (after action command
>>> "show selected only") just
>>> all the molecules from the given solution directly interacting
>>> with previously selected "primary" molecule and it would be a nice
>>> and useful feature I think.
>>>
>>> Perhaps the optimal solution would be to add into "H-bond
>>> Parameters" table an additional "clik choice" which would ensure (if
>>> marked) that together with visualizing of all H-bonds (defined in
>>> the table) will be also selected all molecules which are connected
>>> by that H-bonds.
>>>
>>> (as the supplementary option might be eventually selection of end
>>> residues only (not whole molecules) which might be also useful in
>>> some cases)
>>
>> Hi Marek,
>> This is sort of possible now, depending on whether your molecules
>> are single residues or separate models. Here's the recipe:
>>
>> 1) Find the H-bonds
>> 2) Go to Tools->General Controls and open the Pseudobond Panel
>> 3) Select the hydrogen bonds group in the panel
>> 4) Click the panel's Select Bonded button
>> 5) Use the up arrow key to increase the selection to residues (if
>> your molecules are residues, e.g. water), or use up arrow a few more
>> times if your molecules are models.
>>
>> If your molecules aren't single residues / chains / models then
>> you are kind of stuck, since the selection increase/decrease
>> mechanism doesn't have a "molecule" level per se. Perhaps I could
>> make it so that if you hold the shift key down with up-arrow, the
>> selection changes
>>
>> atom -> residue -> connected fragment (molecule) -> model
>>
>> instead of
>>
>> atom -> residue -> chain (by chain ID) -> model
>>
>> I'll think about it.
>>
>>> #2
>>> Similarly would be cool to have in menu-table "Select -> Zone..."
>>> except
>>>
>>> "Select all atoms/bonds of any residue in selection zone" also
>>> possibility like:
>>>
>>> "Select all atoms/bonds of any MOLECULE having at least one atom in
>>> selection zone".
>>>
>>> Then again using the action "show selected only" one might have
>>> quick and nice
>>> picture only of all and WHOLE molecules which are in the defined
>>> neighbourhood of the
>>> initially selected "primary" molecule.
>>
>> Again, up-arrow could possibly be helpful here. Nonetheless, a
>> useful suggestion.
>>
>>>
>>> #3
>>> Perhaps is it shame :)) but until now I was not able to find the
>>> right button to clear/delete
>>> previously visualized H-bonds.
>>>
>>> So my solution (probably not so much elegant) is that I simply
>>> select one atom (which is
>>> really not the candidate for H-bond ) like C atom and then I ask to
>>> visualize all H-bonds
>>> which has this atom as the one end. So naturally no H-bond is found
>>> and if
>>> I do not mark "Retain currently displayed H-bonds" also the
>>> previously visualized H-bonds
>>> are deleted. But perhaps there is more elegant solution, if not
>>> button so at least some command ?
>>
>> The command "~hb" will remove H-bonds. Also, in the Pseudobond Panel
>> you can close the "hydrogen bonds" group.
>>
>> --Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>> http://www.cgl.ucsf.edu
>>
>>
>>
>>
>>
>> __________ Informace od ESET NOD32 Antivirus, verze databaze 7598
>> (20121017) __________
>>
>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>
>> http://www.eset.cz
>>
>
>
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