Re: [modeller_usage] malign3d will not align multiple structures

[Mark Daniels <>]

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


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
> > 
> > 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: 
> _______________________________________________________________
>
>
>