Hello Oliver-

Thank you for the reply. MALIGN3D does not require an alignment file if the structural models have a 1:1 sequence correspondence. In my case I am aligning five models of the same protein. I figured out what the problem was by looking at the .top files in the examples/tutorial-model folder of modeller6v2. As it turns out, I have to add the command

SET ALIGN_CODES = 'atip' 'atip' 'atip' 'atip' 'atip'

with which MALIGN3D properly loads the five model atip.Bxxx files. The Sanchez and Sali Methods in Molecular Biology article does not mention this (and neither does the manual).

Regards-

Mark J Daniels markjd@scripps.edu

Department of Cell Biology The Scripps Research Institute La Jolla, CA

On Mon, 1 Dec 2003, Oliver Hucke wrote:

> Hi Mark, > > I miss the specification of the alignment file in your top script. I > suppose modeller needs an initial alignment - at least that's how I use > MALIGN3D. The atom files are specified in the alignment file, not in the > script. Please have a look at the example given in the section on > MALIGN3D in the manual. This works fine for me. The initial alignment > can be obtained with the commands SEQUENCE_TO_ALI and MALIGN. > > Hope this helps, > Oliver > > Mark Daniels wrote: > > Hello all- > > > > I'm trying to run malign3d to align multiple models but the routine > > only 'sees' the first structure and does nothing. I'm using the > > malign3d.top file format described in the Sanchez and Sali 2000 Methods > > in Molecular Biology article: > > > > SET OUTPUT_CONTROL = 1 1 1 1 2 > > SET MAXRES = 700 > > SET ATOM_FILES = 'atip.B99990001' 'atip.B99990002' ; > > 'atip.B99990003' 'atip.B99990004' 'atip.B99990005' > > SET WRITE_FIT = on > > MALIGN3D > > > > All the atip.Bxxxx files contain a reasonable structure. Running the > > malign3d.top routine shown above fails to produce any .fit files and > > shows the following error: > > > > openf5__224_> Open 11 OLD SEQUENTIAL atip.B99990001 > > malign3_327W> Only one structure; nothing done. > > > > Would anyone be able to advise me on what I'm missing here or doing wrong? > > > > Thanks in advance- > > > > Mark Daniels > > The Scripps Research Institute > > > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage@salilab.org > > http://salilab.org/mailman/listinfo/modeller_usage > > > -- > _______________________________________________________________ > > Oliver Hucke, Dr. > Health Sciences Building - K418C > University of Washington 1959 NE Pacific St. > Dept. of Biochemistry phone: (206) 685 7046 > Box 357742 fax : (206) 685 7002 > Seattle, WA 98195-7742 email: ohucke@u.washington.edu > _______________________________________________________________ > > >