Dear modellers, [modeller6a] My template contains two disulfides bonds, and the cysteines are conserved in the protein I want to model. Hence, PATCH_SS_TEMPLATE, automatically run by the routine 'model' is suppose to take care of the bonds. It doesn't. Hence my first question: How MODELLER detect SS bonds in templates: SSBOND in the HEADER or CONECT at the end of the PDB file? Then I decided to patch the disulfides manually with INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'a7ggmono2.ali' # alignment filename SET KNOWNS = 'mono2' # codes of the templates SET SEQUENCE = 'a7gg' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling STOP SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '127' '141' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '189' '190' RETURN END_SUBROUTINE It did not work either. Any ideas? -- Dr Nicolas Le Novère http://www-alt.pasteur.fr/~lenov Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK tel: +44 1223 336623 fax: +44 1223 336676 e-mail: nl223@cus.cam.ac.uk