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[dev] quickest way to determine bond distance between polymeric-bonded residues in Pose/Conformation

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[dev] quickest way to determine bond distance between polymeric-bonded residues in Pose/Conformation
#1
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Hi,

I'm trying to determine the bond lengths between consecutive residues in a Pose/Conformation, to determine whether they are actually close enough to be bonded, or if there is a gap between the residues that needs to be closed or filled in. Is there a straightforward way to do this?

Thanks

Category: 
Loop Modeling
Post Situation: 
Unsolved
Thu, 2018-01-18 12:26
ipetrik_ambry
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There's actually a bit of code in Rosetta which does something similar already. It's not encapsulated in an easy-to-use form, but you can potentially crib from it.

This is the code in PoseFromSFRBuilder::build_initial_pose() which handles the `-missing_density_to_jump`. The core of this is as follows: 

core::Real bondlength = ( prev_rsd.atom( prev_rsd.upper_connect_atom() ).xyz() -
          this_rsd.atom( this_rsd.lower_connect_atom() ).xyz() ).length();
if ( bondlength > 3.0 ) {
    // Add TRUNC_VARIANT, as appropriate
}

(Yes, that 3.0 is hard-coded)

Alternatively, you could run with the -missing_density_to_jump option on, and look for residues with the UPPERTERM_TRUNC_VARIANT and LOWERTERM_TRUNC_VARIANT.

 

Tue, 2018-01-30 08:29
rmoretti