Thank you for your feedback. I appreciate your help and also providing access to this freely available program. Basically I've been spending 5,6 hours today on setting up and running this program and got frustrated at some point. I looked at both the manual in the installed folders and online documentation. But it seems that I have to look more carefully since you mentioned my alignment is also not correct. I find all those colons at the second line of the PIR format alignment confusing, maybe it's just me! But anyways I keep trying.

Thanks again, Omid K.

>From: Modeller Caretaker modeller-care@salilab.org >To: Omid Khalouei omid9dr18@hotmail.com >CC: modeller_usage@salilab.org >Subject: Re: [modeller_usage] "Structure not read in" error >Date: Thu, 23 Feb 2006 16:14:20 -0800 > >Omid Khalouei wrote: >>I am just starting to use Modeller. Even though I have a major in computer >>science, have used many bioinformatics tools, and am familiar with Python, >>I haven't been able to figure out how to run this program. To be honest I >>don't find it that user-friendly! > >I suggest you first go through the basic modeling tutorial or at least the >first chapter of the manual on the website; your post strongly suggests >that you haven't done that. Constructive suggestions on how to improve the >documentation and program are, of course, welcomed. > >Obviously there is always room to improve the user-friendliness of the >program, but in your case running a model-default-like script (you didn't >include yours, so I had to guess what you might be doing) gives the >following error in the logfile: >pdbnam__217W> Filename for PDB code not found: 1A8GA > Directories: ./:../atom_files > Extensions : :.atm:.pdb:.ent:.crd >This says that Modeller couldn't find a PDB file called '1A8GA' in either >the current directory or the ../atom_files directory, either as is or with >any of the 4 extensions listed. If this error message isn't clear, let me >know. > >>Basically I'm not sure in which folder I have to put my alignment and PDB >>coordinate files. > >The directory is specified by setting the atom_files_directory variable. >See the simple example at http://salilab.org/modeller/manual/node23.html > >>This is the alignment file that I have created but am not sure if it meets >>the specifications (they both refer to HIV-1 protease, residues 1 to 99 of >>chain A); > >Your alignment file is also not correct. See the URL above for the correct >format. > > Ben Webb, Modeller Caretaker >-- >modeller-care@salilab.org http://www.salilab.org/modeller/ >Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

Omid Khalouei wrote: > This is the end of my log-file: > > #################################################### > Read the alignment from file : 1ZPA-1A8GA.ali > Total number of alignment positions: 99 > > # Code #_Res #_Segm PDB_code Name > ------------------------------------------------------------------------------- > > 1 1A8GA 99 1 1A8GA Comeon > 2 1ZPA 99 1 1ZPA Comeon > runcmd______> alignment.check() > > check_a_343_> >> BEGINNING OF COMMAND > openf5__224_> Open 11 OLD SEQUENTIAL > .\examples\atom_files\1A8GA.pdb > rdpdb___303E> No atoms were read from the specified input PDB file, > since the > starting residue number and/or chain id in MODEL_SEGMENT (or > the alignment file header) was not found; > requested starting position: 1A : > rdabrk__288W> Protein not accepted: 1 > check_a_337E> Structure not read in: 1 > #################################################### > > and here's my alignment file, I followed what I saw on the link that you > sent me. > >> P1;1A8GA > > structureX:1A8GA:1 : :99 : :HIV1 PR: : 1.90: 0.19 > PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD > QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF* > >> P1;1ZPA > > sequence:1ZPA:1 : :99 : :HIV1 PR: : 1.90: 0.19 > PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD > QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF*

Like I said, your alignment file is incorrect. Furthermore, I can't see how that alignment file could generate that error - are you sure that's the one you're using? The error message says that your alignment file is requesting to read the sequence starting at residue '1A' in a chain with no identifier, while the alignment file you've posted requests to read starting from residue '1' in a chain with no identifier. What I suspect you actually want to do is read from residue '1' in chain 'A'. So your alignment header would look something like structureX:1A8GA:1 :A:99 :A:HIV1 PR: : 1.90: 0.19

Ben Webb, Modeller Caretaker

Lucas Bleicher wrote: > I use Modeller for about two years and I can rarely > set up a .PIR file and run the program with no errors > for the first time (and have seen many times questions > on alignment errors here). This is not really > Modeller's manual fault - I think that what causes > most of those errors is that the sequence listed on a > PDB entry does not always correspond to what is really > on the PDB file. Some entries include, for example, > His-tags which are never visible and also residues > which could not be seen on electron density maps and > therefore were not modeled. Setting up the .PIR file > sometimes means to search for missing or modified > residues (e.g. Se-Met or modified Cysteines) on a PDB > and then fix the alignment file, something that can be > really boring in some cases. I have developed a "semi > automatic" approach to do that, but perhaps it would > be interesting to include on newer versions of > modeller a routine to parse the PDB, compare it with > the sequence on the alignment file (which may include > these missing residues) and fix the file.

An excellent suggestion - thanks! I've added it to the Modeller wishlist in the Modeller wiki at: http://salilab.org/modeller/wiki/Wishlist Please feel free to add any similar suggestions to those pages or to this list.

It's difficult to add code to Modeller to fix anything 'automatically', since the PDB is too variable, but we can certainly put in more informative error messages with pointers to where in the PDB the missing residues might be.

Ben Webb, Modeller Caretaker