Hi all,

I've been testing out using Modeller to build ferredoxins (some of the ones in the examples, actually) containing 4Fe-4S cluster(s). I wanted to try different levels of description, so to start out I've been describing the FeS clusters as BLK residues. This works very well for single-template modeling, but when I try to use e.g. 3 template structures, I get 3 times as many atoms in the model cluster as I wanted. I've attached the top and alignment files but there are 3 input atom files (plus the model), so I'll send those on request (in the input atom files I use, the residue names have been changed to BLK and some of the atomnames have been changed from the original pdb, so that they all describe the same position: using the original pdbs should still give you the same problem of excess atoms, but the clusters will be distorted).

Does anyone have a reason for this, or a way out (apart from deleting the 'extra' atoms afterwards)? I'll be building a new FS4 residue anyway; has anyone done that previously?

Many thanks in advance, Lucy Forrest

# Modeller input script # LRF 14mar02 # Build models of 2fdn using 3 template pdbs simultaneously # and multiple alignment # # This script should produce one model, 2fdn.B99990016 # try HETERO atoms #

SYSTEM COMMAND = 'cp 2fdn_3_template_1.ali~ 2fdn_3_template_1.ali'

INCLUDE # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 1

SET ALNFILE = '2fdn_3_template_1.ali'# alignment filename SET KNOWNS = '1DUR' '1BLU' '1CLF' # codes of the templates SET SEQUENCE = '2fdn' # code of the target SET HETATM_IO = 'on' # use Fe/S heteroatoms SET ATOM_FILES_DIRECTORY = '../atom_files.d/' # directories for input pdb SET STARTING_MODEL= 16 # index of the first model SET ENDING_MODEL = 16 # index of the last model SET FINAL_MALIGN3D = '1' # make fitted structures

# thorough MD only #SET MD_LEVEL = 'refine_4'

# Repeat the whole cycle x times and do not stop unless obj.func. > 1E6 SET REPEAT_OPTIMIZATION = 3, MAX_MOLPDF = 1E6

CALL ROUTINE = 'model' # do homology modelling

>P1;1DUR structureX:1DUR:1 :A:102 :A:::-1.00:-1.00 AYVINDSCIACGACKPECPVNCIQEG-SIYAIDADSCIDC------GSCASVCPVGA-----PNPED-------- -----/..* >P1;1BLU structureX:1BLU:1 : :102 : :::-1.00:-1.00 ALMITDECINCDVCEPECPNGAISQGDETYVIEPSLCTECVGHYETSQCVEVCPVDCIIKDPSHEETEDELRAKY ERITG/..* >P1;1CLF structureN:1CLF:1 : :102 : :::-1.00:-1.00 AYKIADSCVSCGACASECPVNAISQGDSIFVIDADTCIDC------GNCANVCPVGAPVQE-------------- -----/..* >P1;2fdn sequence:2fdn:. :.:. : :::-1.00:-1.00 AYVINEACISCGACEPECPVNAISSGDDRYVIDADTCIDC------GACAGVCPVDAPVQA-------------- -----/..*