Re: [modeller_usage] Advice on Modeller usage

[Modeller Caretaker <>]

Nagesh Chakka wrote:
> I am trying to use Modeller to obtain a model using the structure 1XU0.
> I have created the three files needed for Modeller
> In doing so, the final model XlPrP2.B99990004 does not contain all the
> atoms for a particular residue.
>
> For example, the following is the part of the model for one amino acid
>
> ATOM      1  N   ILE     1      14.910   4.779   7.839  1.00 41.08      
> 1SG   2
> ATOM      2  CA  ILE     1      13.848   4.061   8.581  1.00 41.08      
> 1SG   3
> ATOM      3  CB  ILE     1      12.918   3.371   7.630  1.00 41.08      
> 1SG   4
> ATOM      4  CG2 ILE     1      11.924   2.529   8.447  1.00 41.08      
> 1SG   5
> ATOM      5  CG1 ILE     1      12.242   4.416   6.730  1.00 41.08      
> 1SG   6
> ATOM      6  CD1 ILE     1      11.473   3.813   5.557  1.00 41.08      
> 1SG   7
> ATOM      7  C   ILE     1      14.422   3.050   9.510  1.00 41.08      
> 1SG   8
> ATOM      8  O   ILE     1      15.261   2.235   9.128  1.00 41.08      
> 1SG   9
>
> Atoms from the structure file
>
> ATOM      1  N   ILE A 125      15.197  -5.772  -0.208  1.00  0.00        
>   N
> ATOM      2  CA  ILE A 125      14.432  -5.479   0.993  1.00  0.00        
>   C
> ATOM      3  C   ILE A 125      14.890  -6.453   2.086  1.00  0.00        
>   C
> ATOM      4  O   ILE A 125      14.874  -7.667   1.884  1.00  0.00        
>   O
> ATOM      5  CB  ILE A 125      12.922  -5.586   0.661  1.00  0.00        
>   C
> ATOM      6  CG1 ILE A 125      12.526  -4.523  -0.390  1.00  0.00        
>   C
> ATOM      7  CG2 ILE A 125      12.073  -5.416   1.930  1.00  0.00        
>   C
> ATOM      8  CD1 ILE A 125      11.131  -4.703  -1.000  1.00  0.00        
>   C
> ATOM      9  H   ILE A 125      14.783  -6.386  -0.892  1.00  0.00        
>   H
> ATOM     10  HA  ILE A 125      14.656  -4.459   1.305  1.00  0.00        
>   H
> ATOM     11  HB  ILE A 125      12.723  -6.575   0.246  1.00  0.00        
>   H
> ATOM     12 1HG1 ILE A 125      12.591  -3.543   0.075  1.00  0.00        
>   H
> ATOM     13 2HG1 ILE A 125      13.228  -4.540  -1.223  1.00  0.00        
>   H
> ATOM     14 1HG2 ILE A 125      12.338  -4.494   2.447  1.00  0.00        
>   H
> ATOM     15 2HG2 ILE A 125      11.014  -5.400   1.691  1.00  0.00        
>   H
> ATOM     16 3HG2 ILE A 125      12.237  -6.268   2.586  1.00  0.00        
>   H
> ATOM     17 1HD1 ILE A 125      10.989  -3.972  -1.797  1.00  0.00        
>   H
> ATOM     18 2HD1 ILE A 125      11.032  -5.707  -1.414  1.00  0.00        
>   H
> ATOM     19 3HD1 ILE A 125      10.362  -4.542  -0.250  1.00  0.00        
>   H
>
> What is the reason for the loss of the atoms and how can I fix this.

Modeller builds models, by default, using a heavy atom only topology, so 
there are no hydrogen atoms. (Including hydrogen atoms greatly increases 
the CPU time needed to build the models, and generally adds very little 
information, since most templates don't have hydrogen information, so 
the hydrogen positions are largely determined by geometry.)

You can build all hydrogen models by using a different topology library. 
For modern versions of Modeller, just use the 'allhmodel' class 
(http://salilab.org/modeller/manual/node28.html). For old versions using 
TOP, turn on HYDROGEN_IO to read hydrogens from the template structures, 
and set TOPLIB to request the all-atom topology. See 
http://salilab.org/modeller/7v7/FAQ.html#15

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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