Dears, we have an unexplained problem when using the SEQUENCE_TO_ALI command: only the first residue of the MODEL (template) file is transfered to the alignment array, e.g if we write an alignment file, only the first residue appears, though the right number of residues is written by the program (the second line of the alignment file includes the first and last residue number of my pdb file). Here is an example of the output i get when try to test this command on 5fd1:
>P1;all structureX:all: 1 : : 106 : :undefined:undefined:-1.00:-1.00 A*
I would like to precise that we get this problem when using the example loop routine, as well as when simply testing the command e.g: READ_MODEL FILE = '5fd1.ent' SEQUENCE_TO_ALI WRITE_ALIGNMENT FILE='5fd1.ali'
What did we do wrong?
Regards.
Michel Giorgi Lab. Cristallochimie Fac. St. Jerome, Marseille, France