Dear Raghu, Luis, and other Modeller List members,
The problem I recently wrote about with respect to being unable to
read the atom file was solved thanks to Raghu's suggetsion of including
the chain designator plus realigning the sequences with malign. It
wasn;t due to a file-format error.
Thank you Raghu and Luis for writing, and the rest of you for
reading my previous message.
Best wishes,
Rich
On Wed, 12 Mar 2003, Luis Rosales wrote:
> Hi:
>
> >From your output:
>
> > rdpdb___303E> No atoms were read from the specified input PDB file:
> > 1) Possibly because an incorrect/non-existent PDB file is specified.
> > 2) Possibly because the segment is specified incorrectly in the
> > alignment file or by the TOP variable MODEL_SEGMENT. That is,
> > the beginning residue number and/or chain id in
>
> > rdabrk__288W> Protein not accepted: 1
> > rdabrk__290E> Number of residues in the alignment and pdb files are
> > different: 166 0
> > For alignment entry: 1
>
> It seems like modeller is unable to read your pdb template file (it reads o
> residues...), if you imported your file from MS-Dos/Win. that could be the
> problem. (try opening the file in nedit and using the save as... option
> looking that the MS-DOS format option is not selected in the "save as..."
> menu).
> I had the same problem, hope this helps.
>
>
> Luis
>
>
>
--------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Medical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
http://cancercenter.columbia.edu/~friedman/
"You don't have ot do any more work to write a book. You
already wrote a book. Your course notes are a book. I've
seen them lying on the floor of your office. I've seen
course notes used for books on everything from Math to
Origami. Just hand your course notes in. Make sure you
hand in the ones with the apple juice spilled on it."
-Isaac Friedman, age 13
Upon Isaac's attainment of his majority I am discontinuing
the quotes from him.