yes, you need to use a . for each HETATM you include in your ali. The
same for water. They treated separately.
so a PDB file with 2 ion ligands and 4 waters may look like this:
these residues are not selected on the basis of making or not making
but simply following the order as they appear in the PDB file.
"/pipe1/databases/pdb/uncompressed_files/pdb1hci.ent" was our local
setup here, I do not see why it is popping up in your setup.
Frank J A B wrote:
> Dear All
> I'm facing two problems with modeller.
> In the FAQ's question #16 there is an explanation on how to use hetero
> atoms in modelling adding the line HETATM_IO = on in the top script.
> There is also a comment (not clear to me) about the
> use of Ws for water and .s for other atoms in the alignment that still
> remains unsolved to me.
> In my case I'm trying to use FAD during the modelling.
> I can't wonder how to edit the alignment to include this Ws and .s
> I understand that the backslash is a sequence break, but I deduce (not
> sure) that you must to repeat for each residue a symbol like w, . or
> whatever in the same .pir file after the backslash. I didn't find any
> explanation along the manual regard this.
> Check the example given.
> SET ALIGNMENT_FILE = 'align1.ali', KNOWNS='templ1', SEQUENCE='targ1'
> SET HETATM_IO = on, WATER_IO = on
> CALL ROUTINE = 'model'
> The alignment file:
> Need I to repeat the entire alignment (template/target) inside the same
> .pir file (but now using only signs like - , ., w , #) where
> the .s/Ws positions correpond to those aa that make contact with the
> HETATM in the template ?
> The second question is about my log file.
> I'm habituated to use regularly Modeller since version 4 but suddenly the
> job was finished abruptly with this :
> MODELLER 6v2, 17 Feb 2002
> PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
> assgn___544E> Variable name not recognized:
> Command line: INCLUDE
> assgn___525E> Error in TOP variable assignment.
> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
> Is this some kind of bug or a user error ?
> I'm sure that the files are typed correctly (case-sensitive) and the
> folder where the job is started has all the files in it (the tops, ali
> and pdb files).
> I'm not using any file located in the path shown above :
> Any help will be welcome
> Thanks in advance
> Frank Alarcon
> LNCC - Brasil
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras