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
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
participants (2)
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Andras Fiser -
Frank J A B