Subject: CCL software to convert XYZ format to PDB ?

From: Michael <shokhen(at)netvision.net.il>
Date: Wed, 30 Jun 2004 22:11:28 +0200

Dear CCLers,

I need to convert protein structure presented as XYZ (Cartesian coordinate
file)

to the PDB file format.

The problem is that many software packages can do the job but not
completely.

In other words, when such software reads an XYZ file (see the fragment
below):

  N       -1.21000       43.30600      -19.48400

  C       -1.45100       43.83100      -20.83200

  C       -1.89300       45.28700      -20.70900

  O       -1.42200       46.16400      -21.43800

it generates the following PDB analog with unknown residual names and
numbers:

ATOM    462  N   UNK A   1      -1.210  43.306 -19.484  1.00  0.00

ATOM    463  C   UNK A   1      -1.451  43.831 -20.832  1.00  0.00

ATOM    464  C   UNK A   1      -1.893  45.287 -20.709  1.00  0.00

ATOM    465  O   UNK A   1      -1.422  46.164 -21.438  1.00  0.00

while the correct pdb file must specify the residual names and numbers:

ATOM    462  N   VAL    32      -1.210  43.306 -19.484  1.00 14.04
N

ATOM    463  CA  VAL    32      -1.451  43.831 -20.832  1.00  6.48
C

ATOM    464  C   VAL    32      -1.893  45.287 -20.709  1.00  8.17
C

ATOM    465  O   VAL    32      -1.422  46.164 -21.438  1.00 10.91
O

I would highly appreciate if somebody can point me to the reliable free
software for Windows.

Kind regards,

Michael