Hello Elton,

your alignment file states "structure" where it should be "structureX", change it and Modeller should read in the pdb file, as long as you have stored it in the path you gave Modeller in the "SET ATOM_FILES_DIRECTORY"-command. You should also give Modeller the starting/ending aminoacid number and chain number in the alignment file. The second line should be

structureX:1uw3:125:A:230:A:::-1.00:-1.00

Another thing: as long as you do not want to model water or ions, just protein, you should delete all but the aminoacid atoms from the input pdb-file, as modeller will try to match the residues in the alignment file with the pdb-file and will stop if it encounters atoms that are not present in both.

For alignment file parameters, have a look at http://salilab.org/modeller/manual/node72.html

I hope that helps, best wishes,

Thorsten Schweikardt Molecular Biophysics University of Mainz

> -----Original Message----- > From: modeller_usage-bounces@salilab.org > [mailto:modeller_usage-bounces@salilab.org] On Behalf Of > Elton Jose Rosas de Vasconcelos > Sent: Tuesday, July 27, 2004 11:43 PM > To: modeller_usage@salilab.org > Subject: [modeller_usage] Some Doubts > > Dear Doctors and Modeller users, > > We are graduate students in Fortaleza, Brazil and we are > trying to model > an aminoacid sequence deduced from genotyping data using the > MODELLER for > Linux (RedHat 9.0)! Thus, we would like to know if you could > help us on the > script for modelling our target sequence, cause we are having > some troubles > with that. Our log output file stops after the CHECK_ALIGNMENT, in the > BEGINNING OF COMMAND, telling us the template's structure had > not been read. > We put our atomic coordenates files (1uw3.atm and pdb1uw3.ent) into > the /examples/atom_files/ subdirectory. > > Another error message appears when we put, in alignment file > (pri.ali), > "structure" and "sequence" in front of the template and > target sequence > respectively. This error message is "rdpir___648E> Alignment > sequence not found > in PDB file: 1 ../atom_files/pdb1uw3.ent" > > Please check our *.top *.ali and *.log files attached. > > We would appreciate very much if you could give us some light > on solving this > problem. Beforehand I thank you for your attention... > > Vasconcelos, EJR and Nugen (Núcleo de Genômica e > Bioinformática) Group - > Fortaleza, Brazil >