Re: [PyMOL] problems with mutagenesis wizard

[Abhinav V. <abh...@gm...>]

can you give us the exact pdb/code so that we can reproduce the problem ?

On Fri, Jun 1, 2012 at 11:16 AM, James Starlight <jms...@gm...>wrote:

> Dear PyMol users!
>
>
> I've tried to make 1 point mutation by means of pymol's mutagenesis wizard
> and obtain partially broken pdb.
>
> In my caseI've changed 276 residue from Leu to Tyr. As the consequence the
> resulted pdb consist of wrong atom order ( you can see it inthe below where
> new mutaded tyr is mixed with the atoms of the firstr residue and partly
> with the atoms of second residue of that protein ( met-2 and gly-3 in that
> pdb).
>
> ATOM      1  N   MET     2      30.865  33.218  71.898  1.00
> 0.00           N
> ATOM      0  N   TYR   276      36.846  30.673  29.037  1.00
> 0.00           N
> ATOM      2  H   MET     2      30.860  32.973  70.919  1.00
> 0.00           H
> ATOM      1  CA  TYR   276      38.223  31.049  28.728  1.00
> 0.00           C
> ATOM      3  CA  MET     2      30.563  32.110  72.824  1.00
> 0.00           C
> ATOM      2  CB  TYR   276      38.572  32.435  29.346  1.00
> 0.00           C
> ATOM      4  CB  MET     2      29.075  32.007  73.159  1.00
> 0.00           C
> ATOM      3  CG  TYR   276      38.566  32.527  30.876  1.00
> 0.00           C
> ATOM      5  CG  MET     2      28.699  32.785  74.409  1.00
> 0.00           C
> ATOM      4  CD1 TYR   276      39.655  32.065  31.622  1.00
> 0.00           C
> ATOM      6  SD  MET     2      27.037  32.348  75.030  1.00
> 0.00           S
> ATOM      5  CD2 TYR   276      37.467  33.087  31.534  1.00
> 0.00           C
> ATOM      7  CE  MET     2      27.384  30.784  75.811  1.00
> 0.00           C
> ATOM      6  CE1 TYR   276      39.644  32.168  33.011  1.00
> 0.00           C
> ATOM      8  C   MET     2      31.021  30.724  72.375  1.00
> 0.00           C
> ATOM      7  CE2 TYR   276      37.458  33.188  32.922  1.00
> 0.00           C
> ATOM      9  O   MET     2      31.124  30.414  71.189  1.00
> 0.00           O
> ATOM      8  CZ  TYR   276      38.547  32.729  33.660  1.00
> 0.00           C
> ATOM     10  N   GLY     3      31.434  29.985  73.384  1.00
> 0.00           N
> ATOM      9  OH  TYR   276      38.542  32.830  35.022  1.00
> 0.00           O
> ATOM     11  H   GLY     3      31.957  30.390  74.138  1.00
> 0.00           H
> ATOM     10  C   TYR   276      39.196  30.036  29.278  1.00
> 0.00           C
> ATOM     12  CA  GLY     3      31.510  28.518  73.329  1.00
> 0.00           C
> ATOM     11  O   TYR   276      40.317  29.796  28.774  1.00
> 0.00           O
>
>
>
>  As the result when I've tried to process this pdb via Gromacs I've
> obtained incorrect atom numbering etc.  How this error could be fixed ?
>
>
>
> Thanks,
>
> James
>
>
>
>
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