Carlos Luiz N. dos SANTOS wrote: > I am using the basic tutorial steps (1., 2., 3. , 4. , 5.) to > "modeling based on a single template" with my sequence data: > > - I get sucessful at searching for structures related at my > sequence (Step 1), No problems! > > - I do the "STEP 2 - selecting a template" and I find it using > the same tips from the tutorial. No problems again; > > - The problems is in the 'STEP 3 - aligning with the template". > Because I have just the target code at the _aln.pos columm and it is > missing the template code and its data in the cbp20-1h2v.pap result file > (in this message). > > Why ??? I see the "align2d_276_> ALIGN_BLOCK changed to 1" > message at log file (at end of this message) but I did not find the > main raison for it. There are an template and a target. So I think the > ALIGN-BLOCK is 2.
No; ALIGN2D aligns two blocks of sequences with each other. ALIGN_BLOCK denotes the _last_ sequence in the _first_ block. So, with only two sequences, you want to align two blocks of one sequence each - so ALIGN_BLOCK should be 1.
> I used the TOPOLOGY FILE = > '/usr/lib/modeller7v7/modlib/top_heav.lib', but I am not sure that > because there was not this command line at basic example. And if I run > this script wihout this command line the Modeller tell me by warning > that it missing in memory an topology library!
You can read a topology file if you like, but that's not what's causing the problem in this case. Read on...
> SET OUTPUT_CONTROL = 1 1 1 1 1 > SET ATOM_FILES_DIRECTORY = './:../atom_files' > READ_MODEL FILE = '1H2V.pdb' > READ_TOPOLOGY FILE = '/usr/lib/modeller7v7/modlib/top_heav.lib' > SET ADD_SEQUENCE = on > SEQUENCE_TO_ALI ALIGN_CODES = '1H2V' > READ_ALIGNMENT FILE = 'cbp20levure.ali', ALIGN_CODES = 'cbp20', > ADD_SEQUENCE = ON > ALIGN2D > WRITE_ALIGNMENT FILE='cbp20-1h2v.ali', ALIGNMENT_FORMAT = 'PIR' > WRITE_ALIGNMENT FILE='cbp20-1h2v.pap', ALIGNMENT_FORMAT = 'PAP'
You should change the READ_ALIGNMENT call to read: READ_ALIGNMENT FILE = 'cbp20levure.ali', ALIGN_CODES = ALIGN_CODES 'cbp20', ADD_SEQUENCE = ON
I notice the example in the tutorial is incorrect here too. (If you download the basic example .tar.gz, it's OK, but the align2d.top script at http://salilab.org/modeller/tutorial/basic.html was incorrect.) I've just corrected this.
Ben Webb, Modeller Caretaker