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Re: Query,



Hi Pedro,

Dr P.A. Reche wrote:
> 
> Hi there,
> 
> I have a few questions about using modeller. I have been trying to use the
> MALIGN routine of the Modeller package and I have got a few problems.
> Firstly, I am limited to use just five sequences and I would like to know
> how to increase the number of sequences that the program can handle.

The maximum number of sequences is a constant defined at compile time.
The only choice is too use a different modeller executable file. You are
probably using the tiny or small executable. Using the default or huge
executable will allow you to use up to 40 or 101 sequences,
respectively. You can download the executables from our site (
ftp://salilab.org/pub/modeller/ ) . 
The following table comes from the Modeller manual:

http://salilab.org/modeller/manual/node10.html

  b) Array size codes:

---------------------------------------------------------------------
CODE      Max.residues Max.atoms Max.len.alignment Max.numb.sequences
---------------------------------------------------------------------
no code   1000         15000     1000              40
TINY       500         75000      500               5
SMALL     1000         15000     1000               5
HUGE      1000         15000     1000             101
ENORMOUS  2000         30000     2000              40
---------------------------------------------------------------------

> Secondly, I am having some problems runing this routine since I guess that
> the primary homology between my structures is very low. Actually, the
> program runs till this point:
> 
> chkseq__E> sequence difference between alignment and pdb :
>    STRUCTURE RES_IND  ALN_ITYP  ALN_RES  X_ITYP  X_RES  -----*-----
>            4       1         0     ####      12   ASN   -----------
>            4       2         0     ####       3   ASP   -----------
>            4       3         0     ####      20   TYR   -----------
>            4       4         0     ####       5   PHE   -----------
>            4       5         0     ####      15   ARG   -----------
>            4       6         0     ####       1   ALA   -----------
>            4       7         0     ####       3   ASP   -----------
>            4       8         0     ####      16   SER   -----------
>            4       9         0     ####      15   ARG   -----------
>            4      10         0     ####      17   THR   -----------
> fit2xyz_E> number of equivalent positions < 3:     0
> recover__> MODELLER_STATUS >=  STOP_ON_ERROR:   1  1

I have the impression that the sequence in your alignment file does not
correspond exactly to the sequence in the PDB file, for the same
protein, and that is causing the problem. Could you please check if
these is true?

> Will you please tell what is going on. Also, I have a general question. Is
> it possible to  superimpose a set of structures at once (not one to one)?
> and finally is it possible to use MALIGN3D without feeding in the
> script an initial alignment? Thanks a lot.

MALIGN3D will superimpose multiple structures at once. MALIGN3D does
need an initial alignment but it doesn't have to be the correct 3D
alignment. You can feed it a multiple sequence alignment (for instance
created with MALIGN) and then use MALIGN3D to superimpose the structures
and get the "correct" 3D alignment. 

I hope this is useful.

Best Wishes,

Roberto

-- 
Roberto Sanchez              |  phone : (212) 327 7206
The Rockefeller University   |  fax   : (212) 327 7540
1230 York Avenue, Box 38     |  e-mail: 
New York, NY 10021-6399      |  http://salilab.org