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