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
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.