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.
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
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.
Pedro Reche
==============================================================================
Dr. Pedro Antonio Reche Gallardo
Dept. of Biochemistry, U. of Cambridge,
80 Tennis Court Road, CB2 1GA, Cambridge, England, UK
Phone: +44 (0)1223 333662
Fax: +44 (0)1223 333661
http://www-ccmr-nmr.bioc.cam.ac.uk/~par