From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jun 04 2015 - 12:00:24 CDT

Hi Josh:
Yes, index 537 and 510, not 538 and 511. I could have saved your time by
checking graphically what I suspected to be the case. Thanks a lot.

I am impressed by the power of these tcl scripts. It would be great to
arrive at a tcl script capable of describing the volume of protein cavities
during MD.

francesco

On Thu, Jun 4, 2015 at 5:46 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Visualize the selections. You'll find that they are not the same, and so
> naturally the results will be different. See
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node90.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_current_ug_node90.html&d=AwMDaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=-HlUTO-p5cBc5PIIWOaJ9-qnT28s75DUp7XlPlRi7DY&m=e5dWPtI5p2mhpnmvoZ4oBVW-BePpKs1ZV-ak6EsHHWk&s=3zRHZOAHsNlOffZlMWbRv_tx1A_13aCB1P0WNLZaH3Q&e=>
> for the definition of the macros.
>
> -Josh Vermaas
>
>
> On 6/4/15 9:32 AM, Francesco Pietra wrote:
>
> Hello:
>
> In view of use with a homotetramer, I was comparing
> distance.tcl/bigdcd.tcl with resid vs index for a short single chain,
> single dcd.
>
> distance.tcl reads:
>
> source bigdcd.tcl
>
> proc distance { frame } {
> global all sel1 sel2 coord1 coord2 outfile
> set coord1 [lindex [$sel1 get {x y z}] 0]
> set coord2 [lindex [$sel2 get {x y z}] 0]
> puts $outfile "$frame: [vecdist $coord1 $coord2]"
> }
> set outfile [open distance.dat w];
> # set mol [mol new protein.psf waitfor all]
> set mol [mol new blg.psf waitfor all]
> # mol addfile protein.pdb type pdb waitfor all
> mol addfile blg.pdb type pdb waitfor all
> # set sel1 [atomselect $mol "protein and resid 34 and alpha"]
> set sel1 [atomselect $mol "protein and index 511"]
> # set sel2 [atomselect $mol "protein and resid 36 and alpha"]
> set sel2 [atomselect $mol "protein and index 538"]
> bigdcd distance blg.dcd
> bigdcd_wait
> close $outfile
>
> where "index 511" corresponds to resid 34 CA atom and "index 538" to
> resid 36 CA atom.
>
> I wonder whether the discrepancy below listed when using resid vs index
> is acceptable (NOTICE that I used the index for CA as in the PDB file; is
> that correct in the framework of VMD text mode?
>
> vmd -e distance.tcl -dispdev none
>
> distance.dat with resid reads:
> 1: 6.155873294845215
> 2: 6.3324751149574
> 3: 6.267655808391619
> 4: 6.001893779397328
> 5: 5.935921404818315
> 6: 5.75340044561143
> 7: 5.903206322073248
> 8: 6.000084026502264
> 9: 6.123181765569243
> 10: 5.687617330115469
> 11: 5.588952884916724
> 12: 5.621397740963518
> 13: 5.947689151421404
> 14: 6.005809460661218
> 15: 5.892805662838818
> 16: 5.918587368637095
> 17: 6.078843142124178
> 18: 5.829160049190195
> 19: 5.84493097544958
> 20: 6.156780825051894
> 21: 6.089357473930232
> 22: 6.009320894482683
> 23: 6.039823223667995
> 24: 6.131418241840857
> 25: 6.124286431213598
> 26: 6.186483359353395
> 27: 6.195875340907096
> 28: 5.895764830495841
> 29: 6.1294518557292275
> 30: 6.2540777423612335
> 31: 6.197113229710773
> 32: 6.313388207648914
> 33: 6.497207719047839
> 34: 6.456978080128772
> 35: 6.30176524717308
> 36: 6.182407440061586
> 37: 5.939172896709217
> 38: 5.906056737141097
> 39: 6.162640646454019
> 40: 6.279199743063725
> 41: 6.543637151419946
> 42: 6.4449162032242935
> 43: 6.325669741155785
> 44: 6.354868984379231
> 45: 6.457706430729012
> 46: 6.600767128352138
> 47: 6.5583006374750195
> 48: 6.32079177163211
> 49: 6.452229620126813
> 50: 6.496551024801622
> 51: 6.5177934038036645
> 52: 6.429451293884513
> 53: 6.376118267780437
> 54: 6.077281549237033
> 55: 5.854099658958354
> 56: 5.850274767463241
> 57: 6.198129604168876
> 58: 6.0485286244120795
> 59: 6.079240381421482
> 60: 5.9744206773638275
> 61: 6.123270583092752
> 62: 6.005473066549851
> 63: 5.790701277164607
> 64: 5.653011389975589
> 65: 5.461100760290221
> 66: 5.734068473805915
> 67: 6.072277903551858
> 68: 6.069468317908955
> 69: 5.944910088938689
> 70: 5.9141170718072384
> 71: 6.090138817001316
> 72: 5.946905741529113
> 73: 5.829107452677821
> 74: 5.68382532616309
> 75: 5.823621964694188
> 76: 5.767044531468982
> 77: 5.841141572062604
> 78: 5.928387157504003
> 79: 6.023482333243039
> 80: 6.063439927725436
> 81: 6.32053998470388
> 82: 6.341327289040814
> 83: 6.20519775761507
> 84: 6.205142331571849
> 85: 6.122645673605338
> 86: 6.022163609208951
> 87: 6.119559498354708
> 88: 6.079274521721274
> 89: 6.220615535374097
> 90: 6.308776272489288
> 91: 6.136137501190165
> 92: 6.1298573018596905
> 93: 6.018836351487991
> 94: 5.863414168418454
> 95: 6.010756622516953
> 96: 5.956960865296578
> 97: 5.9995292910653975
> 98: 5.949459725963331
> 99: 5.723198191348166
> 100: 6.123118359030882
> 101: 6.131361660031941
> 102: 6.0433403825653125
> 103: 5.8572285953314145
> 104: 5.729594744613678
> 105: 5.841126607065762
> 106: 5.657990071900067
> 107: 5.627232755775197
> 108: 5.609958612253771
> 109: 5.751144979480783
> 110: 5.980132615078155
> 111: 5.988188507430909
> 112: 6.00627161749879
> 113: 6.1774497323435344
> 114: 6.038629865383346
> 115: 6.032425859407662
> 116: 5.891878809119978
> 117: 5.864796880976335
> 118: 5.871247268345111
> 119: 5.9467857173220295
> 120: 5.67542728022883
> 121: 5.574826338779056
> 122: 5.608677369260205
> 123: 5.588631829799197
> 124: 5.633183388382263
> 125: 5.85983612192658
> 126: 5.970173996639731
> 127: 6.232289989558169
> 128: 6.183226667096034
> 129: 5.986306564748091
> 130: 5.8527187295876235
> 131: 5.667387304478913
> 132: 5.6899439458066565
> 133: 5.469971903764231
> 134: 5.5354134421856
> 135: 5.924336859590648
> 136: 5.902510881946771
> 137: 5.812784112515541
> 138: 5.994018048580893
> 139: 5.778274342588817
> 140: 5.846868830559261
> 141: 6.017538249561662
>
>
> while distance.dat with index reads:
> 1: 6.81509667694367
> 2: 7.324764182677088
> 3: 7.069919323694988
> 4: 6.900428779331134
> 5: 6.779582255904655
> 6: 6.6782552979514165
> 7: 6.812071722814608
> 8: 6.821105239039725
> 9: 7.114210320438186
> 10: 6.592142422446802
> 11: 6.128651064070532
> 12: 6.401949561658085
> 13: 6.879654235189838
> 14: 6.981200984844114
> 15: 6.923510281799492
> 16: 6.611598623905179
> 17: 6.704177198345893
> 18: 6.692500627861949
> 19: 6.689484962192078
> 20: 7.093435567839954
> 21: 6.970505723824979
> 22: 6.969242736236588
> 23: 7.015630435244526
> 24: 7.126333502139914
> 25: 7.14371333937126
> 26: 7.205182418657364
> 27: 7.021344698752695
> 28: 6.735458362311062
> 29: 7.0807760874635735
> 30: 7.274808513852262
> 31: 7.348204612566441
> 32: 7.226866649020775
> 33: 7.2774565429363
> 34: 7.161418183211406
> 35: 6.942482885990797
> 36: 6.931180497247215
> 37: 6.655856987063322
> 38: 6.801842519669949
> 39: 7.094670404756691
> 40: 7.177321623425995
> 41: 7.488965388454052
> 42: 7.421950714761952
> 43: 7.328199547379709
> 44: 7.321931128027203
> 45: 7.358071347664505
> 46: 7.393026644932146
> 47: 7.194881981702942
> 48: 6.9221378596130485
> 49: 7.266935873670471
> 50: 7.302311242111963
> 51: 7.3946852634452656
> 52: 7.316321929627676
> 53: 7.424162388205278
> 54: 7.06378853192656
> 55: 7.001706179549798
> 56: 6.986406120219026
> 57: 7.437136197425969
> 58: 7.237961221846839
> 59: 7.1695717193011905
> 60: 7.092589620751929
> 61: 7.057414866572976
> 62: 6.839492425930564
> 63: 6.6690875175306035
> 64: 6.5751768692617425
> 65: 6.405488894058185
> 66: 6.7391106816201365
> 67: 6.973626178415096
> 68: 7.289031136655081
> 69: 6.876845434473571
> 70: 6.987305144524046
> 71: 7.0774340716118935
> 72: 7.010224910843495
> 73: 6.873840911774636
> 74: 6.716127781766796
> 75: 6.738170363183688
> 76: 6.766809505258355
> 77: 6.786923860345665
> 78: 7.073969821356074
> 79: 7.091126106383393
> 80: 7.0465595059673305
> 81: 7.3873687524421365
> 82: 7.349306524781023
> 83: 7.336652772510283
> 84: 7.409495907622654
> 85: 7.165156902098029
> 86: 7.2507191352372145
> 87: 7.287430091085758
> 88: 7.275026744776622
> 89: 7.383866182257686
> 90: 7.517982670845706
> 91: 7.423334543688227
> 92: 7.34049534731532
> 93: 7.242669391693693
> 94: 7.024874571499522
> 95: 7.027173323603344
> 96: 7.077856913208377
> 97: 7.167091364510184
> 98: 7.139585426436412
> 99: 6.707798939556049
> 100: 7.284049342902034
> 101: 7.313782733381586
> 102: 7.223773237696821
> 103: 6.729890932705325
> 104: 6.775945212544188
> 105: 6.980054229815082
> 106: 6.877712153627434
> 107: 6.790306528332171
> 108: 6.748034371956233
> 109: 7.05441887523652
> 110: 7.0834718734935675
> 111: 6.924383617625959
> 112: 7.138870200754995
> 113: 7.054282927996913
> 114: 7.322920189215957
> 115: 7.234087982730475
> 116: 6.952640803525461
> 117: 7.060739238101184
> 118: 7.128465696658351
> 119: 7.152363790442598
> 120: 6.704962573386964
> 121: 6.631226126227999
> 122: 6.664512745103688
> 123: 6.684939700297468
> 124: 6.404532936068054
> 125: 6.989098340683407
> 126: 6.9912134498442775
> 127: 7.102676661789097
> 128: 7.3124875709405375
> 129: 7.067251234024886
> 130: 6.805250013051595
> 131: 6.827058024108577
> 132: 6.790603362828231
> 133: 6.551860606998993
> 134: 6.697579121333028
> 135: 7.145316428896854
> 136: 7.033859385577582
> 137: 6.901371663073955
> 138: 6.93716503862458
> 139: 6.796286816824731
> 140: 6.737236609644235
> 141: 6.970489721535678
>
>
>