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 <jmsstarlight@gmail.com> 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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