Elliott Stollar wrote: > I have looked at the manual and previous queries posted on this > reoccuring subject but am unable to get modeller to model a protein-DNA > complex where I treat the DNA as a rigid body. > > All I get back are models of the protein with no DNA present.
1. Use Modeller 9v1, which has much improved support for ligands. 2. Use a Python script to build your model - TOP has been deprecated for a long time. 3. See http://salilab.org/modeller/9v1/manual/node18.html for an input file to build a model with HETATM residues preserved as rigid bodies.
There is no need to modify your PDB file, unless it is obviously non-standard in some way. As long as your DNA is in HETATM records, Modeller should pick it up just fine.
> 2. Included in my alignment file a '.' for each BLK residue and a '/' to > signifiy the end of a chain > > >P1;9ANT > structureX:9ANT:FIRST :@ END : : :dros:undefined: 2.4: 0.23 > RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK/ > .............../ > ...............*
This part is fine...
> >P1;1AAA > sequence:1AAA:FIRST :@ END : : :human:undefined: 0.00: 0.00 > RTAYTNTQLLELEKEFHFNKYLCRPRRVEIAALLDLTERKVKVWFQNRRMKHKRQTQ*
Your models don't contain the DNA, because you're not listing it in the target sequence here. The DNA ligands and/or chain breaks also need to be in your target sequence. See the URL above for an example alignment.
Ben Webb, Modeller Caretaker