Hi
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:
>P1;1abc JSDHFLSKJAGHSALKJ/..wwww*
these residues are not selected on the basis of making or not making contact, 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.
Andras
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. > > INCLUDE > SET ALIGNMENT_FILE = 'align1.ali', KNOWNS='templ1', SEQUENCE='targ1' > SET HETATM_IO = on, WATER_IO = on > CALL ROUTINE = 'model' > > The alignment file: > > >P1;templ1 > structureX:templ1:1::10:: > FAYVI/.wwww* > > >P1;targ1 > sequence:targ1:1::8:: > -GWIV/.ww-w* > > 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: > /pipe1/databases/pdb/uncompressed_files/pdb1hci.ent > 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 : > /pipe1/databases/pdb/uncompressed_files/pdb1hci.ent > > Any help will be welcome > > Thanks in advance > > Frank Alarcon > LNCC - Brasil > www.lncc.br