[gmx-users] select in pymol after trjconv

[Justin A. Lemkul]

ZHAO Lina wrote:
> ATOM    397  N   ALA    48      35.480  52.940  57.920  1.00  
> 0.00           
> ATOM    398  H   ALA    48      34.740  52.570  57.360  1.00  
> 0.00           
> ATOM    399  CA  ALA    48      36.190  54.120  57.430  1.00  
> 0.00           
> ATOM    400  CB  ALA    48      35.900  55.320  58.350  1.00  
> 0.00           
> ATOM    401  C   ALA    48      37.690  53.840  57.260  1.00  
> 0.00           
> ATOM    402  O1  ALA    48      38.120  52.590  57.580  1.00  
> 0.00           
> ATOM    403  O2  ALA    48      38.460  54.860  56.810  1.00  
> 0.00           
> ATOM    404  N   ASP     1       7.960  12.190  74.660  1.00  
> 0.00           
> ATOM    405  H1  ASP     1       8.090  11.710  75.530  1.00  
> 0.00           
> ATOM    406  H2  ASP     1       7.210  12.840  74.760  1.00  
> 0.00           
> ATOM    407  H3  ASP     1       7.730  11.520  73.950  1.00  
> 0.00           
> ATOM    408  CA  ASP     1       9.190  12.900  74.290  1.00  
> 0.00           
> ATOM    409  CB  ASP     1      10.390  11.940  74.180  1.00  
> 0.00           
> ATOM    410  CG  ASP     1      10.860  11.380  75.510  1.00  
> 0.00           
> ATOM    411  OD1 ASP     1      10.420  11.850  76.560  1.00  
> 0.00           
> ATOM    412  OD2 ASP     1      11.880  10.480  75.450  1.00  
> 0.00           
> ATOM    413  C   ASP     1       9.000  13.630  72.970  1.00  
> 0.00           
> ATOM    414  O   ASP     1       8.580  13.010  71.990  1.00  0.00 
> 
> 
>          
> 
> 
>     I'm guessing you have different chain identifiers, i.e. identical
>     chains, just labeled A and B or something?
> 
> 
> I got four chains. and the .pdb from trjconv do not distinguish those 
> things and don't show chain info.
> 
> Do you have some nice way to view .gro in pymol. (compare VMD I am a bit 
> familiar with pymol)
> 

Renumber using genconf.  You should be able to select consecutive residues in 
this way.  Otherwise, use a couple quick text editor tricks to write in chain 
identifiers to make selection easy.

-Justin

> Thanks again,
> 
> lina
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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