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Re: [modeller_usage] align2d again

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
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
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