Alternate Conformations

The following examples show how to set up alternate conformations for structure factor calculations as well as for empirical energy calculations.

The first step is to append the alternate conformations to the current molecular structure file. In this particular case, one wants to generate alternate conformations for the side chains of residues 1 and 7.

alternate.inp

Now one has to go to the graphics and move the alternate conformations into the correct positions. In subsequent protocols, one has to insert the following statement after reading the molecular structure file:

 
constraints  
   inter = ( segid "MAIN" ) ( segid "MAIN" ) 
   inter = ( segid "MAIN" or segid "ALT1" ) ( segid "ALT1"  ) 
   inter = ( segid "MAIN" or segid "ALT2" ) ( segid "ALT2" ) 
end

In this example it is assumed that the segment identifier "MAIN" refers to the molecular structure before alternate conformations were included; "MAIN" can be substituted by the user if it is required. The constraints interaction statements make sure that the alternate conformations do not interact with each other but rather interact only with the remaining molecular structure.

The next step is to set occupancies of the alternate conformations

vector do (q=0.5) ( segid "ALT1" )
vector do (q=0.5) ( segid "ALT2" )

Now one is ready to carry out structure factor calculations as well as empirical energy calculations. In order to refine occupancies, one should use the xrefin optimize group statement.

xrefin
   optimize group
      q=( segid "ALT1" and resid 1 ) 
      q=( segid "ALT2" and resid 1 ) 
      q=( segid "ALT1" and resid 7 ) 
      q=( segid "ALT2" and resid 7 ) 
       nstep=15
       drop=1
    end
end

Note that at present the occupancy refinement procedure does not constrain the sum of occupancies to be one. Manual resetting of the occupancies may be required.