Subject: CCL: software to convert XYZ format to PDB ?

From: Michael <shokhen[at]netvision.net.il>
Date: Wed, 30 Jun 2004 23:26:32 +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

---

From: Eric Bennett <ericb)at(pobox.com>
Date: Wed, 30 Jun 2004 17:39:15 -0500

Michael wrote:

>...
I just wrote a perl script to do this a couple weeks ago... you can 
download a free perl interpreter for Windows from www.perl.com.
http://www.perl.com/download.csp

Here's the script, it's very short:
http://abacavir.pharmacy.umn.edu/~bennette/software/text-to-pdb.txt

-- 
Eric Bennett, Center for Drug Design, U of Minnesota

The whole aim of practical politics is to keep the populace alarmed,
and hence clamorous to be led to safety, by menacing it with an endless
series of hobgoblins, all of them imaginary. -H.L. Mencken