[Biopython] geometry.py

[Frederico Moraes Ferreira]

Hi João,
I was pretended by your print commands in the end of the 
calculate_shape_param function. Looking closer to your code, the outputs 
are the ellipsoid' s semi-axes. Even though, if I double them some large 
discrepancies appear when compared with the maximum dimension of the 
shape. I have tested those functions for a considerable number of pdbs 
and wouldn't expecting a perfect match either. However, there are some 
discrepancies which should be investigated. Here goes some of them:
################################
S_1AVSA_29_0004_1.pdb
#Dimensions(a,b,c) #Rg #Anisotropy
36.30 76.0 170.03 42.43 0.51
Dmax: 133.07

S_1AVSA_29_0004_10.pdb
#Dimensions(a,b,c) #Rg #Anisotropy
37.10 52.63 62.49 20.06 0.07
Dmax: 70.58

S_1AVSA_29_0004_11.pdb
#Dimensions(a,b,c) #Rg #Anisotropy
38.94 52.74 81.96 23.47 0.18
Dmax: 104.99

S_1AVSA_29_0004_12.pdb
#Dimensions(a,b,c) #Rg #Anisotropy
36.59 54.33 127.19 31.99 0.47
Dmax: 104.18

S_1AVSA_29_0004_13.pdb
#Dimensions(a,b,c) #Rg #Anisotropy
33.14 52.26 76.41 21.99 0.19
Dmax: 81.21

S_1AVSA_29_0004_14.pdb
#Dimensions(a,b,c) #Rg #Anisotropy
39.52 54.42 121.81 31.11 0.43
Dmax: 104.17

S_1AVSA_29_0004_16.pdb
#Dimensions(a,b,c) #Rg #Anisotropy
34.10 53.17 176.35 41.89 0.69
Dmax: 131.53

S_1AVSA_29_0004_17.pdb
#Dimensions(a,b,c) #Rg #Anisotropy
31.73 74.31 101.41 28.99 0.23
Dmax: 90.38
#################################

All the Best,
Fred

P.S.: here goes code to calculate Dmax (https://gist.github.com/2854563)


Em 01-06-2012 04:03, João Rodrigues escreveu:
>
> Hi Frederico,
>
> From what I understand, those dimensions are those of the smallest 
> ellipsoid that fits your structure. I would therefore not expect a 
> perfect match. Ezgi can answer better for sure.
>
> How do you calculate the dimensions yourself?
>
> Best,
>
> João
>
> No dia 31 de Mai de 2012 20:55, "Frederico Moraes Ferreira" 
> <ferreirafm at usp.br <mailto:ferreirafm at usp.br>> escreveu:
>
>     Hi João,
>     The gyration radio (Rg) is running just fine. They are in
>     excellent agreement with those from some models I have tested.
>     However, the maximum dimensions do not match at all. Did orientate
>     the model before tensor analysis?
>     Fred
>
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