From: chiessi_at_uniroma2.it
Date: Fri Jul 23 2021 - 04:42:54 CDT

Dear Rui, Josh, Axel

thank you very much for all your input!
Now the problem is clear and also how to fix it

Sincerely

Ester

Joaquim Rui de Castro Rodrigues <joaquim.rodrigues_at_ipleiria.pt> ha scritto:

> Dear Ester,
>
> This is because the selection returned by atomselect is ordered by
> index. To use "measure dihed", you should make 4 atomselections,
> each one having only one atom:
> set a1 [atomselect top "name O4"]
> set a2 [atomselect top "name C1"]
> set a3 [atomselect top "name O8"]
> set a4 [atomselect top "name C10"]
> measure dihed "[$a1 get index] [$a2 get index] [$a3 get index] [$a4
> get index]"
>
> Best regards,
> Rui Rodrigues
>
>
>
> ________________________________
> De: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> em nome de
> chiessi_at_uniroma2.it <chiessi_at_uniroma2.it>
> Enviado: 22 de julho de 2021 11:55
> Para: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> Cc: ester.chiessi_at_uniroma2.it <ester.chiessi_at_uniroma2.it>
> Assunto: vmd-l: Discrepancy in value of dihedral angles of a sugar
> molecule by VMD tools
>
> Good morning
>
> Working with this molecule (the coordinated in PDB format are at the
> end of the message) I noticed that the value of some dihedral angles
> is different depending on the method I used to measure it. I used:
> a) the pick with mouse of the four atoms, that gives the value of
> the dihedral
> b) the line command "measure dihed"
>
> The results obtained with a) and b) methods are listed below for the
> anomalous dihedrals:
>
> Info) Added new Dihedrals label MOL1:O4/MOL1:C1/MOL1:O8/MOL1:C10 = -96.387154
> measure dihed [[atomselect top "name O4 C1 O8 C10"] get index]
> 103.36381530761719
>
> Info) Added new Dihedrals label MOL1:O15/MOL1:C13/MOL1:O20/MOL1:C22 =
> -106.423363
> measure dihed [[atomselect top "name O15 C13 O20 C22"] get index]
> 94.68035125732422
>
> Info) Added new Dihedrals label MOL1:O9/MOL1:C7/MOL1:O14/MOL1:C16 =
> -106.413147
> measure dihed [[atomselect top "name O9 C7 O14 C16"] get index]
> 96.04247283935547
>
> Info) Added new Dihedrals label MOL1:C10/MOL1:O8/MOL1:C1/MOL1:C2 = 143.676331
> measure dihed [[atomselect top "name C10 O8 C1 C2"] get index]
> -38.713417053222656
>
> By inspecting the molecule it is evident that the right value is that
> obtained with a).
>
> However, I would like to understand if I am wrong in something when
> using "measure dihed". For many other dihedral angles in this molecule
> I get the same value with a) and b) methods.
>
> Thanks for any suggestion
>
> Ester
>
> __________________
>
> TITLE Grunge ROck MAChoS
> MODEL 1
> ATOM 1 C1 MOL 1 -6.016 -0.209 -0.093 0.298667.00
> C
> ATOM 2 O4 MOL 1 -6.490 1.115 0.205 -0.546499.00
> O
> ATOM 3 O8 MOL 1 -4.796 -0.367 0.552 -0.395148.00
> O
> ATOM 4 C10 MOL 1 -3.593 -0.134 -0.198 0.087925.00
> C
> ATOM 5 C9 MOL 1 -3.133 1.316 0.016 0.042422.00
> C
> ATOM 6 C8 MOL 1 -1.713 1.534 -0.515 0.318595.00
> C
> ATOM 7 C7 MOL 1 -0.779 0.436 0.030 0.257354.00
> C
> ATOM 8 O9 MOL 1 -1.289 -0.839 -0.320 -0.443242.00
> O
> ATOM 9 C11 MOL 1 -2.551 -1.143 0.292 0.042531.00
> C
> ATOM 10 C12 MOL 1 -2.870 -2.639 -0.043 0.875354.00
> C
> ATOM 11 O10 MOL 1 -3.967 -2.883 -0.632 -0.825435.00
> O
> ATOM 12 O11 MOL 1 -1.995 -3.460 0.299 -0.825435.00
> O
> ATOM 13 H23 MOL 1 -2.458 -1.054 1.388 0.066513.00
> H
> ATOM 14 O14 MOL 1 0.479 0.573 -0.565 -0.488503.00
> O
> ATOM 15 C16 MOL 1 1.646 0.491 0.254 0.205766.00
> C
> ATOM 16 C15 MOL 1 2.254 -0.917 0.246 0.251145.00
> C
> ATOM 17 C14 MOL 1 3.669 -0.913 0.833 0.023633.00
> C
> ATOM 18 C13 MOL 1 4.535 0.106 0.099 0.201172.00
> C
> ATOM 19 O15 MOL 1 3.941 1.391 0.254 -0.331659.00
> O
> ATOM 20 C17 MOL 1 2.641 1.517 -0.338 -0.035713.00
> C
> ATOM 21 C18 MOL 1 2.218 2.961 -0.075 0.213947.00
> C
> ATOM 22 O16 MOL 1 2.202 3.254 1.319 -0.695593.00
> O
> ATOM 23 H30 MOL 1 3.082 3.006 1.653 0.429254.00
> H
> ATOM 24 H10 MOL 1 1.202 3.118 -0.443 0.045148.00
> H
> ATOM 25 H11 MOL 1 2.906 3.630 -0.612 0.045148.00
> H
> ATOM 26 H27 MOL 1 2.703 1.347 -1.424 0.095652.00
> H
> ATOM 27 O20 MOL 1 5.799 0.146 0.678 -0.388791.00
> O
> ATOM 28 C22 MOL 1 6.928 0.170 -0.211 0.028042.00
> C
> ATOM 29 C21 MOL 1 7.436 -1.265 -0.414 0.245591.00
> C
> ATOM 30 C20 MOL 1 8.735 -1.246 -1.217 0.164784.00
> C
> ATOM 31 C19 MOL 1 9.749 -0.314 -0.525 0.091943.00
> C
> ATOM 32 O17 MOL 1 10.142 -0.934 0.674 -0.40459.00
> O
> ATOM 33 C26 MOL 1 11.241 -0.295 1.322 -0.044241.00
> C
> ATOM 34 H41 MOL 1 11.474 -0.893 2.205 0.092539.00
> H
> ATOM 35 H42 MOL 1 10.988 0.726 1.628 0.092539.00
> H
> ATOM 36 H43 MOL 1 12.119 -0.263 0.662 0.092539.00
> H
> ATOM 37 O21 MOL 1 9.221 0.985 -0.332 -0.453004.00
> O
> ATOM 38 C23 MOL 1 8.008 1.050 0.441 0.305403.00
> C
> ATOM 39 C24 MOL 1 7.613 2.516 0.523 -0.39280.00
> C
> ATOM 40 H14 MOL 1 6.675 2.621 1.074 0.107484.00
> H
> ATOM 41 H15 MOL 1 7.476 2.930 -0.483 0.107484.00
> H
> ATOM 42 H16 MOL 1 8.390 3.094 1.033 0.107484.00
> H
> ATOM 43 H35 MOL 1 8.201 0.659 1.450 0.086243.00
> H
> ATOM 44 H12 MOL 1 10.621 -0.154 -1.176 0.172951.00
> H
> ATOM 45 O18 MOL 1 8.443 -0.768 -2.526 -0.682910.00
> O
> ATOM 46 H31 MOL 1 9.247 -0.858 -3.062 0.45668.00
> H
> ATOM 47 H13 MOL 1 9.155 -2.260 -1.254 0.088685.00
> H
> ATOM 48 O19 MOL 1 6.484 -2.086 -1.073 -0.688366.00
> O
> ATOM 49 H32 MOL 1 5.757 -2.264 -0.441 0.425346.00
> H
> ATOM 50 H36 MOL 1 7.674 -1.674 0.579 0.042562.00
> H
> ATOM 51 H37 MOL 1 6.638 0.600 -1.176 0.158716.00
> H
> ATOM 52 H34 MOL 1 4.598 -0.148 -0.969 0.11912.00
> H
> ATOM 53 O12 MOL 1 4.259 -2.205 0.710 -0.623962.00
> O
> ATOM 54 H28 MOL 1 3.540 -2.848 0.852 0.437287.00
> H
> ATOM 55 H33 MOL 1 3.634 -0.615 1.893 0.116235.00
> H
> ATOM 56 O13 MOL 1 1.469 -1.910 0.904 -0.67336.00
> O
> ATOM 57 H29 MOL 1 1.326 -1.626 1.824 0.437362.00
> H
> ATOM 58 H26 MOL 1 2.312 -1.256 -0.795 0.106824.00
> H
> ATOM 59 H9 MOL 1 1.410 0.793 1.283 0.068972.00
> H
> ATOM 60 H7 MOL 1 -0.699 0.519 1.128 0.094327.00
> H
> ATOM 61 O6 MOL 1 -1.230 2.842 -0.233 -0.673471.00
> O
> ATOM 62 H24 MOL 1 -1.274 2.981 0.729 0.444322.00
> H
> ATOM 63 H21 MOL 1 -1.716 1.451 -1.607 0.112573.00
> H
> ATOM 64 O7 MOL 1 -3.998 2.245 -0.621 -0.718937.00
> O
> ATOM 65 H25 MOL 1 -4.896 2.085 -0.267 0.48174.00
> H
> ATOM 66 H22 MOL 1 -3.119 1.493 1.107 0.083692.00
> H
> ATOM 67 H8 MOL 1 -3.784 -0.305 -1.263 0.105353.00
> H
> ATOM 68 H1 MOL 1 -5.907 -0.316 -1.183 0.095651.00
> H
> ATOM 69 C2 MOL 1 -6.974 -1.276 0.447 0.066474.00
> C
> ATOM 70 O1 MOL 1 -6.573 -2.556 0.003 -0.621853.00
> O
> ATOM 71 H18 MOL 1 -5.582 -2.588 -0.074 0.402987.00
> H
> ATOM 72 H17 MOL 1 -6.947 -1.201 1.547 0.099043.00
> H
> ATOM 73 C3 MOL 1 -8.418 -1.020 -0.011 0.119218.00
> C
> ATOM 74 O2 MOL 1 -9.334 -1.843 0.704 -0.437022.00
> O
> ATOM 75 C25 MOL 1 -9.668 -3.069 0.066 0.116232.00
> C
> ATOM 76 H38 MOL 1 -10.421 -3.552 0.694 0.038712.00
> H
> ATOM 77 H39 MOL 1 -8.798 -3.727 -0.034 0.038712.00
> H
> ATOM 78 H40 MOL 1 -10.098 -2.894 -0.932 0.038712.00
> H
> ATOM 79 H2 MOL 1 -8.485 -1.234 -1.089 0.099146.00
> H
> ATOM 80 C4 MOL 1 -8.834 0.437 0.207 0.20254.00
> C
> ATOM 81 O3 MOL 1 -10.090 0.636 -0.428 -0.715397.00
> O
> ATOM 82 H19 MOL 1 -10.232 1.604 -0.430 0.439005.00
> H
> ATOM 83 H3 MOL 1 -8.909 0.616 1.293 0.058444.00
> H
> ATOM 84 C5 MOL 1 -7.773 1.398 -0.365 0.229691.00
> C
> ATOM 85 H4 MOL 1 -7.738 1.271 -1.459 0.036496.00
> H
> ATOM 86 C6 MOL 1 -8.056 2.868 -0.027 0.203684.00
> C
> ATOM 87 H5 MOL 1 -7.252 3.500 -0.422 0.054588.00
> H
> ATOM 88 H6 MOL 1 -8.084 2.989 1.060 0.054588.00
> H
> ATOM 89 O5 MOL 1 -9.334 3.300 -0.510 -0.704953.00
> O
> ATOM 90 H20 MOL 1 -9.262 3.438 -1.469 0.45311.00
> H
> TER
> ENDMDL
>
>
>
>
>
>
>
>
> --
> Ester Chiessi
> Department of Chemical Sciences and Technologies
> University of Rome Tor Vergata
> Via della Ricerca Scientifica
> 00133 Rome (Italy)
> E-mail: ester.chiessi_at_uniroma2.it
> tel +39 6 72594462
>
>
> Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle
> linee guida del Garante per posta elettronica e interne (artt. 2 e 15
> Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art.
> 49 Codice dell’amministrazione digitale) si precisa che le
> informazioni contenute in questo messaggio -come pure i dati esteriori
> delle comunicazioni e i file allegati- sono riservate e ad uso
> esclusivo del destinatario. Divulgazione, copia, stampa o qualunque
> altro uso da parte di altri non è autorizzato. Qualora il messaggio in
> parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza
> copiarlo e di non inoltrarlo a terzi, dandocene gentilmente
> comunicazione al seguente indirizzo e-mail privacy_at_uniroma2.it
> <mailto:privacy_at_uniroma2.it> .
>
> On the basis of “(UE) Rules 2016/679 and the codes in general
> guidelines of Garante for electronic and internal mail (artt. 2 e 15
> Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art.
> 49 Codice dell’amministrazione digitale) information here contained
> and any attachments is confidential and intended for the recipient(s)
> only. Dissemination, copying, printing or use by anybody else is
> unauthorized. If you are not the intended recipient, please delete
> this message and any attachments and advise the sender by return
> e-mail to privacy_at_uniroma2.it <mailto:privacy_at_uniroma2.it> .

-- 
Ester Chiessi
Department of Chemical Sciences and Technologies
University of Rome Tor Vergata
Via della Ricerca Scientifica
00133 Rome (Italy)
E-mail: ester.chiessi_at_uniroma2.it
tel +39 6 72594462
Ai sensi del Regolamento (UE) 2016/679 e dei principi contenuti nelle  
linee guida del Garante per posta elettronica e interne (artt. 2 e 15  
Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art.  
49 Codice dell’amministrazione digitale) si precisa che le  
informazioni contenute in questo messaggio -come pure i dati esteriori  
delle comunicazioni e i file allegati- sono riservate e ad uso  
esclusivo del destinatario. Divulgazione, copia, stampa o qualunque  
altro uso da parte di altri non è autorizzato. Qualora il messaggio in  
parola Le fosse pervenuto per errore, La preghiamo di eliminarlo senza  
copiarlo e di non inoltrarlo a terzi, dandocene gentilmente  
comunicazione al seguente indirizzo e-mail privacy_at_uniroma2.it  
<mailto:privacy_at_uniroma2.it> .
On the basis of “(UE) Rules 2016/679 and the codes in general  
guidelines of Garante for electronic and internal mail (artt. 2 e 15  
Cost.; Corte cost. 17 luglio 1998, n. 281 e 11 marzo 1993, n. 81; art.  
49 Codice dell’amministrazione digitale) information here contained  
and any attachments is confidential and intended for the recipient(s)  
only. Dissemination, copying, printing or use by anybody else is  
unauthorized. If you are not the intended recipient, please delete  
this message and any attachments and advise the sender by return  
e-mail to privacy_at_uniroma2.it <mailto:privacy_at_uniroma2.it> .