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 par@mole.bio.cam.ac.uk http://www-ccmr-nmr.bioc.cam.ac.uk/~par