Hi modellers

I want to build a model of a protein-DNA complex. I'd like to include the DNA somehow in Modeller's calculations so that the side chains of DNA-ligating residues don't overlap with the DNA; it doesn't need to be any more detailed than that. >From the manual and __homcsr.top, if I understand correctly, the presence of DNA as either HETATM or as BLK residues would produce some distance restraints that would help stop the protein overlapping the DNA. The problem is that I can't get the program to read in either HETATM or BLK residues.

As I understand it, it should be necessary just to say

SET HETATM_IO ON

for HETATMs to be read in. However, even when I include this, and with the actual atoms in the pdb file in any number of formats (before/after the protein, with/without chain terminators), there are never any HETATMs selected. When the program reaches the hetatm_restraints subroutine I get

------------------------------------------------------------------------

TOP______> 191 167 PICK_ATOMS PICK_ATOMS_SET = 3, ATOM_TYPES = 'ALL', RES_TY; PES = 'HET'

Number of atoms to choose from, total : 1372 1372 Atom types to be searched for (ATOM_TYPES) : ALL Residue types to be searched for (RES_TYPES) : HET Selection mode (SELECTION_MODE) : ATOM What to do with atoms & sets (SELECTION_STATUS): INITIALIZE SEGMENT search; residue range (2i5,2a5) : 1 178 1: 178: Selection residue step (SELECTION_STEP) : 1

selatm___> Number of selected atoms : 0

List of segments of contiguous residues with at least one selected atom:

SEGMENT RNUM AA --- RNUM AA LEN

------------------------------------------------------------------------

Likewise, when I define the DNA as BLK residues e.g.

ATOM 1123 P BLK D 17 144.632 59.838 30.258 1.00 27.98 ATOM 1124 O1P BLK D 17 145.093 59.652 31.638 1.00 27.57 ATOM 1125 O2P BLK D 17 144.499 58.295 29.675 1.00 28.96 ATOM 1126 O5* BLK D 17 144.790 60.781 29.234 1.00 26.16 ATOM 1127 C5* BLK D 17 144.578 60.298 27.868 1.00 25.22 ATOM 1128 C4* BLK D 17 144.388 61.601 27.149 1.00 24.34 ATOM 1129 O4* BLK D 17 143.191 62.224 27.722 1.00 24.36 ATOM 1130 C3* BLK D 17 145.497 62.594 27.338 1.00 24.62 ATOM 1131 O3* BLK D 17 145.740 63.280 26.082 1.00 26.54 ATOM 1132 C2* BLK D 17 144.928 63.498 28.477 1.00 23.75 ATOM 1133 C1* BLK D 17 143.473 63.562 28.036 1.00 22.08 ATOM 1134 N9 BLK D 17 142.569 64.122 29.049 1.00 21.02 ATOM 1135 C8 BLK D 17 142.641 64.249 30.366 1.00 19.45 ATOM 1136 N7 BLK D 17 141.558 64.720 30.956 1.00 19.95 ATOM 1137 C5 BLK D 17 140.778 65.088 29.838 1.00 20.06 ATOM 1138 C6 BLK D 17 139.544 65.807 29.768 1.00 18.89 ATOM 1139 O6 BLK D 17 138.950 66.253 30.736 1.00 18.64 ATOM 1140 N1 BLK D 17 139.135 66.022 28.510 1.00 18.84 ATOM 1141 C2 BLK D 17 139.783 65.638 27.382 1.00 18.86 ATOM 1142 N2 BLK D 17 139.238 65.889 26.180 1.00 18.54 ATOM 1143 N3 BLK D 17 140.930 64.925 27.382 1.00 19.84 ATOM 1144 C4 BLK D 17 141.387 64.761 28.668 1.00 19.99

using an alignment file like

>P1;2bop_dimer_DNAblk structureX:2bop_dimer_DNAblk: 326:A: 17:D: ---SCFALISGT-ANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSP--SQRQDFLK HVPLPPGMNISG-FTASLDF/ ---SCFALISGT-ANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSP--SQRQDFLK HVPLPPGMNISG-FTASLDF/ ................./ .................*

the BLK residues are not read in and the blk_restraints subroutine finds no atoms to restrain.

What am I doing wrong? Thanks a lot in advance

Daniel Rigden