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) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/
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