error parsing ATOM record when coordinate long-ish
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I can't read a particular atom line that looks like: ATOM 4 CA GLY A 4 -32.686-186.362 -1.715 1.00 20.00 C I presume that the reason is that the y-coordinate forms a continuous string with the x-coordinate. However, this line complies with the PDB format; I quote from the RCBS site: 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms I realize that this may be seldom a problem, but I think it should be tackled. In my case, this is a dummy atom to represent a dipole moment vector with quite a big magnitude. I have the same problem in the last and the previous snapshot versions of chimera (both in linux and MacOSX) Thank you in advance, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork@yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (Darwin) iD8DBQFGD2QuF6oOrDvhbQIRApSSAJ94MwNKKsPowzYE/k61g9Yen1PArwCfSnWJ gUXmMlHVsrRuLscR3IWg/tQ= =6/U1 -----END PGP SIGNATURE-----
On Apr 1, 2007, at 12:50 AM, Miguel Ortiz-Lombardia wrote:
I can't read a particular atom line that looks like:
ATOM 4 CA GLY A 4 -32.686-186.362 -1.715 1.00 20.00 C
I presume that the reason is that the y-coordinate forms a continuous string with the x-coordinate. However, this line complies with the PDB format; I quote from the RCBS site:
39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms
Hi Miguel, The problem isn't with the numbers running together, it's that they're in the wrong columns. If you count it out, you'll find that your Y coordinate is in columns 38-45 rather than 39-46. This becomes obvious if you put your line next to one from a standard PDB file (such as 1GCN, below): ATOM 4 CA GLY A 4 -32.686-186.362 -1.715 1.00 20.00 ATOM 1 N HIS 1 49.668 24.248 10.436 1.00 25.00 1 1GCN 50 If I insert a space before the start of your coordinates, Chimera reads the line okay. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
participants (2)
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Eric Pettersen -
Miguel Ortiz-Lombardia