[PyMOL] problems with mutagenesis wizard II

[Carola S. H. <Car...@ru...>]

Dear all,

I recently upgraded to Ubuntu 12.04 (pymol version 1.4.1-3). Since I did
the upgrade, mutations done with the mutagenesis wizard lead to
incorrect atom numbering in the saved pdb file. Before, the problem
definitely did not exist. I read the recent post in this forum
concerning this, but the pymol version 1.4 seems to lead to this
problem, too.

Here an example:

ATOM      1  N   MET A   7      72.739 -17.539   8.852  1.00 36.46
N  
TER       2      MET A   7 
ATOM      0  N   ALA A  12      77.920  -8.244  14.624  1.00  0.00
N  
TER       1      ALA A  12 
ATOM      2  CA  MET A   7      73.836 -17.058   9.739  1.00 35.87
C  
TER       3      MET A   7 
ATOM      1  CA  ALA A  12      77.603  -6.935  15.187  1.00  0.00
C  
TER       2      ALA A  12 
ATOM      3  C   MET A   7      74.382 -18.171  10.623  1.00 36.04
C  
TER       4      MET A   7 
ATOM      2  CB  ALA A  12      78.933  -6.222  15.489  1.00  0.00
C  
TER       3      ALA A  12 
ATOM      4  O   MET A   7      73.676 -18.689  11.489  1.00 36.57
O  
TER       5      MET A   7 
ATOM      3  C   ALA A  12      76.716  -6.146  14.255  1.00  0.00
C  
TER       4      ALA A  12 
ATOM      5  CB  MET A   7      73.338 -15.921  10.634  1.00 34.58
C  
TER       6      MET A   7 
ATOM      4  O   ALA A  12      77.070  -6.025  13.073  1.00  0.00
O  
TER       5      ALA A  12 
ATOM      6  CG  MET A   7      72.989 -14.645   9.899  1.00 33.55
C  
ATOM      7  SD  MET A   7      72.558 -13.328  11.053  1.00 30.82
S  
ATOM      8  CE  MET A   7      74.184 -12.785  11.572  1.00 31.08
C  
ATOM      9  N   THR A   8      75.645 -18.528  10.413  1.00 36.23
N  
ATOM     10  CA  THR A   8      76.278 -19.573  11.207  1.00 35.81
C  
ATOM     11  C   THR A   8      76.461 -19.071  12.633  1.00 34.75
C  
ATOM     12  O   THR A   8      76.529 -19.861  13.578  1.00 35.68
O  
ATOM     13  CB  THR A   8      77.662 -19.947  10.646  1.00 37.30
C  
ATOM     14  OG1 THR A   8      78.530 -18.810  10.723  1.00 38.49
O  
ATOM     15  CG2 THR A   8      77.544 -20.390   9.196  1.00 38.06
C  
ATOM     16  N   GLY A   9      76.539 -17.750  12.779  1.00 32.20
N  
ATOM     17  CA  GLY A   9      76.713 -17.161  14.096  1.00 27.95
C  
ATOM     18  C   GLY A   9      76.334 -15.690  14.126  1.00 24.78
C  
ATOM     19  O   GLY A   9      76.080 -15.092  13.083  1.00 24.20
O  

[...]

Can somebody help me out?

Thanks in advance,

Caro