[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

What's the best way to deal with DNA?



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