VMD-L Mailing List

From: Nithin Rai (nithin_at_mblab.gla.ac.uk)
Date: Tue Oct 07 1997 - 04:12:06 CDT

Dear all..

I'm a little baffled as to why two seperate files,
both of which are minimalised versions of pdb files,
are read differently.

The first file is a portion of the cranbin.pdb file.
The portion of the structure that is
displayed still retains the spatial information held
by the complete file.

cranbin.pdb

ATOM 17.047 14.099 3.625
ATOM 16.967 12.784 4.338
ATOM 15.685 12.755 5.133
ATOM 15.268 13.825 5.594
ATOM 18.170 12.703 5.337
ATOM 19.334 12.829 4.463
ATOM 18.150 11.546 6.304
ATOM 15.115 11.555 5.265
ATOM 13.856 11.469 6.066
ATOM 14.164 10.785 7.379
ATOM 14.993 9.862 7.443
ATOM 12.732 10.711 5.261
ATOM 13.308 9.439 4.926
ATOM 12.484 11.442 3.895
ATOM 13.488 11.241 8.417
ATOM 13.660 10.707 9.787
END

This 2nd file is one I made up (see below). As far as I can tell, it
shares the same format as the above file, but appears to be
read differently. At the first instance, this is shown by
the labels attributed to each atom; in the 2nd file the labels
correspond to bits of the co-ordinates, where as for the first file, there
appears to be no labelling.

The_one_i_made_up.pdb

ATOM 18.169 10.516 7.887
ATOM 16.686 14.695 8.168
ATOM 18.823 10.177 1.217
ATOM 19.523 13.992 4.815
ATOM 9.610 8.962 9.714
ATOM 28.050 18.324 9.225
ATOM 19.223 8.571 4.014
ATOM 9.733 7.956 5.567
ATOM 9.388 8.570 4.219
ATOM 19.595 9.067 6.595
ATOM 10.580 9.587 7.117
ATOM 8.364 7.460 6.912
ATOM 17.590 9.036 6.488
END

Does anyone know the reason why the second file is read differently
to the first?

Thanking you in advance for what might be an embarrassingly simple
explanation.

Nithin