[PyMOL] save molecule format

Fri, 13 Feb 2004 15:57:33 -0800

All-
    When using the Pymol ability to save a structure as a PDB file it appears that the "standard" PDB format is changed in at least one instance.  When a sidechain has more than one conformation in the crystal structure (A, B), the saved PDB file will have the two conformations before the amide of the group instead of after.
    Doing nothing more than loading and then saving a structure to a new file yields the following results.
Original file:
ATOM     87  N   SER A  13       2.735   9.167  21.169  1.00  9.31           N
ATOM     88  CA  SER A  13       2.455   9.048  19.752  1.00 10.35           C
ATOM     89  C   SER A  13       1.623  10.233  19.278  1.00  9.48           C
ATOM     90  O   SER A  13       1.775  10.681  18.144  1.00 10.31           O
ATOM     91  CB ASER A  13       1.719   7.737  19.462  0.34 10.21           C
ATOM     92  CB BSER A  13       1.705   7.743  19.467  0.66 14.26           C
ATOM     93  OG ASER A  13       2.552   6.621  19.728  0.34 11.15           O
ATOM     94  OG BSER A  13       0.474   7.699  20.166  0.66 22.03           O

After saving to pdb:
ATOM     87  CB ASER A  13       1.719   7.737  19.462  0.34 10.21           C
ATOM     88  OG ASER A  13       2.552   6.621  19.728  0.34 11.15           O
ATOM     89  CB BSER A  13       1.705   7.743  19.467  0.66 14.26           C
ATOM     90  OG BSER A  13       0.474   7.699  20.166  0.66 22.03           O
ATOM     91  N   SER A  13       2.735   9.167  21.169  1.00  9.31           N
ATOM     92  CA  SER A  13       2.455   9.048  19.752  1.00 10.35           C
ATOM     93  C   SER A  13       1.623  10.233  19.278  1.00  9.48           C
ATOM     94  O   SER A  13       1.775  10.681  18.144  1.00 10.31           O

As far as I can tell it only happens with those sidechains with multiple conformations.  Anyone else have this problem?  Is there a quick fix?

Pymol 0.93 on Fedora Core 1.

Thanks.
Eric Zollars

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